Xpert QA Guide 2019

Practical Guide to
Implementing a
Quality Assurance
System for Xpert
MTB/RIF Testing
(“Xpert QA Guide”)
Practical Guide to
Implementing a
Quality Assurance
System for Xpert
MTB/RIF Testing
(“Xpert QA Guide”)
Contents
Acknowledgements iv
Disclaimer iv
Acronyms and Abbreviations v
Glossary of terms vi
About this guide vii
Target audience viii
Background 1
Introduction to quality assurance and continuous quality improvement 2
Standards and key activities for assuring quality 3
From standards and procedures to implementation 5
Part 1: National and supervisory levels 6

Background 6
Element 1. Governance 8
Element 2. Strategic planning 11
2.1. Understanding the current quality of the Xpert MTB/RIF testing network 11
2.2. Prioritize interventions 13
2.3. Set the budget and time line 14
Element 3. Quality procedures and documentation 15
Element 4: Training, competency assessment and certification 17
4.1 Develop a national training curriculum for the Xpert MTB/RIF test 17
4.2. Perform competency assessments 18
Element 5. Data connectivity and remote monitoring 20
Element 6. A safe and functional testing site 23
Element 7. Equipment and supplies 25
7.1. Equipment service and maintenance 25
7.2 Quality supplies 26
8. External quality assessment (EQA) 27
8.1. On-site supervision 27
8.2. Proficiency testing 28
Element 9. Monitor performance of Xpert MTB/RIF testing and of the QA/CQI system 30
9.1 Establish an M&E framework for Xpert MTB/RIF testing and for the QA system 30
9.2 Assign responsibilities for data collection, reporting and analysis 34
9.3 Collect, compile and analyse data 35
9.4 Evaluate progress and identify trends 36
Element 10. Strengthen the clinical-laboratory interface and the diagnostic cascade 37
ii
Practical Guide to Implementing a Quality Assurance System for Xpert MTB/RIF Testing
Part 2: QA for Xpert MTB/RIF testing sites 38
Standards and key activities for assuring quality 38
Element 1. Governance 42
Element 2. Planning 43
2.1. Situational analysis 43
2.2. Budget 43
Element 3. Quality procedures and documentation 44
Element 4. Training, competency assessment and certification 46
4.1. Provide training for Xpert MTB/RIF users, advanced users, and clinicians 46
4.2. Conduct and document competency assessments 47
Element 5. Diagnostics connectivity and remote monitoring 49
Element 6. A safe and functional testing site 51
6.1. Create and maintain a functional working environment 51
6.2. Create and maintain a safe working environment 52
Element 7. Equipment and supplies 55
7.1. Maintenance and calibration of the Genexpert instrument 55
7.2. Ensure adequate supplies & reagents 57
Element 8. Participate in an EQA programme 59
8.1. Participate in a system of supportive supervision and on-site evaluations 59
8.2. Test PT panels 60
Element 9. Monitor and analyse Xpert MTB/RIF quality indicators 61
9.1. Identify and implement quality indicator monitoring 61
9.2. Regularly review quality indicators and troubleshoot unexpected results
by identifying corrective actions 64
9.3. Report quality indicator data to the NTP/MOH 65
Element 10. Strengthen the clinical-laboratory interface and the diagnostic cascade 66
10.1. Provide training on the diagnostic cascade to laboratorians and health care workers 66
10.2. Test quality samples 67
10.3. Report accurate results 69
Additional resources 73
List of Supporting Documents/Forms and Templates 75
Notes 76
iii
Acknowledgements
This guide is substantially based on a pre-publication version which was developed and piloted by
the Foundation for Innovative New Diagnostics (FIND) and the U.S. Centers for Disease Control and
Prevention (CDC), with funding from the United States President’s Emergency Plan for AIDS Relief
(PEPFAR) under Cooperative Agreement 3U2GPS002746. The following people contributed to the
development and review of the original version:
Lead writers: André Trollip and Heidi Albert (FIND, Cape Town, South Africa). Reviewers: Heather
Alexander, Kyle DeGruy, Patricia Hall, Peter Minchella, Bill Coggin (CDC), Daniela Cirillo, Elisa Tagliani
(San Raffaele Scientific Institute, Milan, Italy), Martina Casenghi (Médecins Sans Frontières-Access
Campaign, Geneva, Switzerland), Kekeletso Kao, Jesse Wambugu (FIND, Geneva, Switzerland).
Revision and finalization of the guide: led by Thomas Shinnick (independent consultant), Heidi Albert
(FIND, South Africa) and Josephine San Pedro (CDC) with technical contributions from Andre Trollip
(FIND, South Africa), Kyle DeGruy and Patricia Hall (CDC). Critical review was provided by members
of the Global Laboratory Initiative (GLI) Core Group, including Lice Gonzalez Angulo, Maka Akhalaia,
Kathleen England, Marguerite Massinga Loembe, Alaine Umubyeyi Nyaruhirira and Abiola Tubi. Copy
editing: Beatrice Gordis (FIND, Switzerland).
The revision and finalization of the guide was made possible through funding from the African
Society for Laboratory Medicine (ASLM) as part of a project supported by the United States President’s
Emergency Plan for AIDS Relief (PEPFAR) under Grant No.NU2GGH000710.
Disclaimer
The mention of specific companies or of certain manufacturers’ products does not imply that they are
recommended in preference to others of a similar nature that are not mentioned. Errors and omissions
excepted, the names of proprietary products are distinguished by initial capital letters.
All reasonable precautions have been taken to verify the information contained in this publication.
However, the published material is being distributed without warranty of any kind, either expressed
or implied. The responsibility for the interpretation and use of the material lies with the reader. In no
event shall there be liability for damages arising from its use. The findings and conclusions in this report
are those of the authors and do not necessarily represent the official position of the Centers for Disease
Control and Prevention/ The Agency for Toxic Substances and Disease Registry.
iv
Acronyms and Abbreviations
AFB Acid-fast bacilli
CDC U.S. Centers for Disease Control and Prevention
CQI Continuous quality improvement
DCS Dried culture spots
DNA Deoxyribonucleic acid
DST Drug susceptibility testing
DTS Dried tube spot
EQA External Quality Assurance / Assessment
GLI Global Laboratory Initiative
ISO International Organization for Standardization
M&E Monitoring and evaluation
MDR-TB Multidrug-resistant tuberculosis
MGIT Mycobacteria Growth Indicator Tube
MOH Ministry of Health
MTBC Mycobacterium tuberculosis complex
NHLS National Health Laboratory Service
NTP National TB Programme
NTRL National TB Reference Laboratory
PPE Personal protective equipment
PT Proficiency testing
QA Quality assurance
QC Quality control
QMS Quality management system
RIF Rifampicin
SOP Standard operating procedure
TB Tuberculosis
TWG Technical working group
TOT Training of Trainers
WHO World Health Organization
WRD WHO-recommended rapid TB diagnostic
Glossary of terms
What is it? Why do you need it? How does it work?
QA covers the entire

test process, from pre-
Sum total of all testing site analytical to analytical &
Quality assurance activities undertaken to To ensure quality diagnostic post-analytical, including
(QA) ensure accurate & reliable results. sample collection, transport,
results. personnel, procedures,
processes, equipment,
environment & reagents.
QC materials are made to

Measures put in place during To ensure that the
mimic patient samples &
the testing phase to ensure information generated by
Quality control are tested with the patient
the procedure assures the testing site is accurate,
(QC)- see also IQC samples to evaluate the
quality results; e.g., known reliable & reproducible
examination component.
negative & positive slides for & serves as a mechanism
[ISO 15189 Positive controls have
every staining batch. Testing by which testing sites can
Clause 5.6.2] known reactivity & negative
site staff performs QC validate the competency of
controls are nonreactive for
concurrently during testing. their diagnostic services.
the test being evaluated.
To ensure the most Data collection, analysis &

effective & long-lasting creative problem solving
Quality
Process of continuous improvements by are key components of
improvement
analysis, & remedial & anticipating & preventing this process that involves
preventative action to problems before they occur, identification of defects,
[ISO 15189 Clause
improve quality. rather than by identifying & followed by remedial action
4.1.1.4]
correcting defects after they to prevent recurrence of
arise. problems.
To ensure that testing sites Testing sites are visited by

Onsite supervisory run smoothly & to motivate qualified personnel & are
Direct supervision
visits technicians to improve or evaluated using standardized
maintain performance. checklists.
Performance indicators
Performance
can be used to monitor
indicators Performance indicators are To give an objective
all activities from sample
objective measures of testing viewpoint of the structure &
receipt to the time the
[ISO 15189 site practices. processes of the testing site.
patient is placed on
Clause 4.14.7]
treatment.
Internal quality Similar to QC; the ISO

control (IQC) standard indicates that these
terms are sometimes used See QC See QC
[ISO 15189 interchangeably in different
Clause 5.6.2] settings.
Users are tested theoretically

Competency & practically to determine
assessment To determine whether users if they have sufficient
A theoretical & practical test
are following a procedure as understanding of the test
to determine proficiency.
[ISO 15189 Clause documented in the SOP. procedure to troubleshoot
5.1.6] problems that may arise
during testing.
Test results reported by each

Proficiency testing An independent & unbiased
testing site are compared
(PT) or Quality assessment of the testing
To assure the quality of to the reference test results.
Assessment performance at of the
the results generated at the The testing site is then
testing site. Provides an
testing site. provided with a report
[ISO 15189 assessment of the validity of
indicating the accuracy of
Clause 5.6.3] testing at the testing site.
their results.
vi
About this guide
The Practical Guide to Implementing a Quality Assurance System for Xpert MTB/RIF Testing (Xpert QA Guide)
provides practical guidance and tools to establish and implement a quality assurance (QA) system for the
Xpert MTB/RIF test across the diagnostic network. Such a system is designed to ensure the following are
in place and sustained:
• All testing is done in compliance with national testing algorithms and standard operating
procedures (SOP)s;
• A cadre of competent users is available to perform the test;
• Testing sites provide uninterrupted diagnostic services and testing services are unaffected by
stock-outs and module failures;
• Good quality samples are collected, quality testing is done in a timely manner and the Xpert MTB/RIF
test results are reported without delay;
• Technical assistance, guidance and on-site supportive supervision are provided to testing sites, in
particular those that need it most;
• The TB diagnostic network is monitored, using electronic systems where possible, and the collected
data are analysed, evaluated and used to inform decision-making.
The strategies and approaches described in this document are not unique to the Xpert MTB/RIF test.
This guide can therefore be used to inform development of a quality improvement approach for other
tests using the GeneXpert platform, as well as other molecular, near point-of-care and point-of-care,
instrument-based diagnostic tests or platforms.
vii
Target audience
This guide is intended for implementers of the Xpert MTB/RIF test and QA managers across the
laboratory diagnostic network. Specifically, this guide is intended to inform Ministry of Health officials,
National TB Programme officials, National TB Reference Laboratory personnel, donors, implementing
partners, QA unit personnel, programme managers, testing site managers, supervisory staff and
GeneXpert users at national, regional or testing site level on the how to implement activities to assure the
quality of Xpert MTB/RIF results.
Part 1 of the guide (National and Supervisory Levels) focuses on establishing or integrating Xpert MTB/
RIF QA activities into the TB diagnostic network in a country or region and Part 2 (QA at Xpert MTB/
RIF Testing Sites) addresses key activities to be carried out at the testing sites to ensure the production of
quality Xpert MTB/RIF results. Each part is divided into sections, each dealing with an aspect of assuring
a quality Xpert MTB/RIF test result. Links are provided to supporting documents, checklists, forms and
training materials.
Note: In this guide, the term ‘testing site’ is used to denote a site where the Xpert MTB/RIF test is being
performed and includes both traditional laboratories and point-of-care or other clinical testing sites
where the Xpert MTB/RIF test is being performed. Furthermore, to ensure the quality of the overall
diagnostic process, some of the QA processes (e.g., use of SOPs, participation in supervisory visits,
monitoring performance indicators, training, etc.) target activities at participating clinical sites (e.g.,
specimen collection sites, sample referral centers, clinics).
Note: In this guide, the term Xpert MTB/RIF test is used to denote either the Xpert MTB/RIF test or the
Xpert MTB/RIF Ultra test. When the two tests differ (e.g., whether or not a ‘trace’ result is generated), the
tests will be described separately.
viii
Background
The World Health Organization (WHO) End TB Strategy calls for an end to the global tuberculosis
(TB) epidemic, aiming to reduce deaths by 95%, cut new TB cases by 90%, and ensure that no family
is burdened with catastrophic expenses due to TB (WHO, 2014)1. Despite TB mortality having fallen
globally by 47% since 1990, it remains the world’s top infectious killers of our time, claiming more than
1.6 million lives in 2017 alone (WHO, 2018)2. Many people die from TB due to delayed diagnosis and
treatment initiation.
The End TB Strategy highlights the critical role of laboratories in the post-2015 era and emphasizes that
in order to meet the targets of the End TB Strategy, WHO-recommended rapid TB diagnostics (WRDs)
should be available to all persons with signs or symptoms of TB; all bacteriologically confirmed TB
patients should receive drug-susceptibility testing (DST) at least for rifampicin (RIF); and fluroquinolone
resistance should be ruled out, preferably using WRDs3. The Xpert MTB/RIF® test is a cartridge-based,
automated WRD run on the GeneXpert® platform (Cepheid Inc.; Sunnyvale, CA, USA). The test can
simultaneously detect Mycobacterium tuberculosis complex bacteria (MTBC) and resistance to RIF in less
than two hours. Since its launch in 2010, a total of 29,865 instrument modules and more than 23 million
Xpert MTB/RIF cartridges have been procured in 130 high TB burden developing countries (Cepheid
data, December 2016).
The Xpert MTB/RIF test has the potential to significantly decrease diagnostic delays, increase the
detection of drug resistance and impact TB transmission. However, there are a variety of challenges to
providing quality Xpert MTB/RIF results:
• Inadequate training and mentoring

• Lack of, or poor adherence to, standard operating procedures (SOPs)
• Stock-outs and use of expired reagents
• Absent or inadequate maintenance of equipment
• Poor quality of samples being tested
• Lack of regular on-site supportive supervision
• Lack of monitoring and evaluation of the TB diagnostic network
Failure to provide a quality Xpert MTB/RIF result can result in either under- or over-diagnosis of TB.
Under-diagnosis (i.e., a falsely negative result) can lead to worsening of disease and can contribute to the
spread of TB (including drug-resistant TB) in the community (Bailey, 2011)4. Over-diagnosis (i.e., a falsely
positive result) may result in unnecessary patient treatment and stigma. False results can also undermine
confidence in laboratory testing and lead to delayed diagnosis and reduce use of laboratory data for
patient care decisions.
A laboratory test is just one part of the diagnostic process which starts with the patient experiencing
symptoms and deciding to seek care (i.e., passive case finding) or a healthcare worker identifying a
person to be evaluated for TB (i.e., active case finding). At this point, the healthcare worker refers the
specimen to the laboratory, where it is analysed. The results of the test are sent to the healthcare worker,
who initiates appropriate treatment and monitors response to therapy. A lack of quality or delays in any
of the steps in this process can reduce the clinical and public health impact of laboratory testing. As such
a system to ensure the quality of laboratory testing must address all the relevant parts of the diagnostic
cascade, not just what happens in the laboratory.
1 The End TB Strategy – Global strategy and targets for tuberculosis prevention, care and control after 2015.
http://www.who.int/tb/strategy/End_TB_Strategy.pdf
2 Global tuberculosis report 2018. Geneva: World Health Organization; 2018. WHO/CDS/TB/2018.20.
https://www.who.int/tb/publications/global_report/en/
3 World Health Organization. WHO consolidated guidelines on drug-resistant tuberculosis treatment.
https://apps.who.int/iris/bitstream/handle/10665/311389/9789241550529-eng.pdf?ua=1
4 Bailey S.L., Roper M.H., Huayta M., Trejos N., López Alarcón V. & Moore D.A. 2011. Missed opportunities for tuberculosis diagnosis. Int J Tuberc Lung
Dis 15: 205-10
Figure 1: The TB diagnostic cascade
Diagnostic network
Laboratory services
Introduction to quality assurance and continuous quality improvement
Quality Xpert MTB/RIF test results are essential to ensure patients are correctly diagnosed in a timely
manner and rapidly initiated on an appropriate treatment regimen.
Quality assurance (QA) is a system that monitors the various aspects of a diagnostic process ensuring that the
results it produces are accurate, reliable and timely.
Implementation of quality assurance (QA) activities across the TB diagnostic network is part of the
continuous quality improvement (CQI) process. CQI is a cyclical, continuous process-based, data-driven
approach to improving the quality of diagnostic testing.
CQI operates under the belief that there is always room for improving operations, processes and activities to
increase quality.
Figure 2: Continuous quality improvement process
1. Plan
3. Monitor 2. Implement
• The PLAN phase includes establishing a governance structure for QA activities, assembling a QA
management team, conducting situational analysis of current QA activities, setting quality targets and
developing an action plan for their implementation.
• The IMPLEMENT phase includes implementing QA and quality improvement activities in a phased
manner at both existing and new testing sites.
• The MONITOR phase includes establishing a monitoring and evaluation (M&E) framework to
monitor the diagnostic network; assigning responsibilities for data collection, analysis and reporting;
collecting and analyzing data; and evaluating progress toward established targets.
Standards and key activities for assuring quality
Quality standards are goals toward which efforts and resources to assure quality Xpert MTB/RIF testing
should be directed. Standards that were developed to measure the performance of the TB diagnostic
network form the basis of the standards for the Xpert MTB/RIF QA system. The TB diagnostic network
standards are based on criteria developed by the Global Laboratory Initiative (GLI) for ensuring the
quality of acid-fast bacilli (AFB) smear microscopy5, by the African Society of Laboratory Medicine
(ASLM) and the Association of Public Health Laboratories (APHL) for evaluating diagnostic networks6,
and by USAID and partners for evaluating TB diagnostic networks in Nigeria and India7. The standards,
associated QA activities and corresponding sections of this guide are described in Table 1.
5 TB Microscopy Network Accreditation. An assessment tool. Global Laboratory Initiative. 2013. http://www.stoptb.org/wg/gli/assets/documents/TB-
Microscopy_Network_Accreditation_Web.pdf
6 Ondoa, P. et al. A new matrix for scoring the functionality of national laboratory networks in Africa: introducing the LABNET scorecard. African
Journal of Laboratory Medicine, 5, Oct. 2016. http://www.ajlmonline.org/index.php/ajlm/article/view/498/712
7 Albert, H. Essential standards for a TB diagnostic network. ASLM2016.
Table 1: Diagnostic network standards and key quality assurance activities
Diagnostic Network Standards Key QA Activities
Governance (Element 1)8

• Establish procedures & structures with clearly defined roles &
responsibilities
Structures & policies are in place that enable
• Appoint, train & empower quality officers
continuous, country-wide availability of
Planning (Element 2)
free, quality assured diagnosis according to
• Conduct a situational analysis
the national guidelines.
• Develop a prioritized action plan for phased implementation of
the required QA activities
• Adequately budget for QA activities
A minimum package of tests & quality QA documentation (Element 3)

standards is defined for each level of the TB • Use standardized documents, records & forms for recording &
diagnostic network. reporting sample requests & results at all testing sites
Training & certification (Element 4)

Adequate numbers of competent, well-
• Adopt standardized curricula for trainings
trained & motivated technical & managerial
• Train at least two users per site; assess competency
staff are available at all levels of the
• Train sufficient advanced users to provide supervision &
diagnostic network.
advanced troubleshooting
Inter-operable & inter-connected electronic

Data connectivity & remote monitoring (Element 5)
recording & reporting systems are in
• Utilize remote monitoring systems to collect & analyse data
place that generate reliable data that are
relating to performance indicators, QA & supplies management
monitored & analysed in real time.
A safe & functional testing site (Element 6)

• Assess each testing site for suitability and readiness prior to
Testing is performed in a manner & in
GeneXpert installation using a standardized checklist
facilities that ensure the safety of the staff,
• Ensure that the site is not hazardous for the staff, patient,
customers, community & environment.
community or environment
• Ensure that a good working environment is available
Supply chain (Element 7)

• Ensure uninterrupted supply of Xpert MTB/RIF supplies &
reagents
Testing is performed with state-of-the-
• Perform new lot testing on new batches of reagents
art, well-maintained equipment & an
Equipment servicing and maintenance (Element 7)
uninterrupted supply of quality reagents &
• Ensure that all GeneXpert instruments undergo routine
consumables.
maintenance & calibration
• Verify all instruments are fit for use at installation, after service or
calibration, or after moving instruments
Proficiency testing (PT) (Element 8)

• Enroll each testing site in a PT programme
• Provide testing sites with timely feedback from PT events
• Investigate incorrect PT results & take corrective actions
Site supervision (Element 8)
Continuous quality improvement targets
• Assess each testing site for readiness prior to GeneXpert
all facilities within the network & includes
installation using a standardized checklist
quality indicator monitoring, external
• Make on-site supervisory visits on a regular basis (at least yearly)
quality assurance & regular on-site
by competent personnel
supervision.
Monitoring & evaluation (Element 9)
• Collect, analyse and report performance indicator data monthly
for trends that may inform operational decisions
• Review performance indicator data locally & nationally to inform
overall programme planning & improvement
8 The element numbers correspond to the numbers of the sections in Part 1 and Part 2 of this guide that describe the activities needed to accomplish
the standard.
Diagnostic Network Standards Key QA Activities
Strengthen the clinical-laboratory interface & the diagnostic

cascade (Element 10)
• Provide training on all aspects of the diagnostic cascade that
affects the quality of TB testing to all laboratorians, clinicians,
nurses & other healthcare providers
An efficient diagnostic-clinical interface • Ensure that national testing algorithms are followed & that the
allows for appropriate diagnostic tests to be correct test is ordered for each patient
ordered & performed, & ensures the timely • Ensure that quality specimens are collected, properly labelled,
linkage of diagnosed patients to appropriate correctly stored, & promptly transported to the testing site
care & treatment. • Enforce the use of standardized test requisition forms; ensure
that they are completed with all the required information
• Report accurate results to clinicians & TB & MDR-TB treatment
focal persons; include information on the interpretation of test
results. Use standardized reporting forms
• Monitor performance of the diagnostic cascade
From standards and procedures to implementation
A QA system targets all facilities within the diagnostic network (e.g., clinics, specimen collection and
referral sites, testing laboratories, treatment centers, etc.) and all the pertinent steps in the diagnostic
cascade. A comprehensive QA system includes standardized procedures (i.e., SOPs), document control,
quality indicator monitoring, internal quality controls, external quality assessment, proficiency testing,
regular on-site supervision, as well as timely feedback, corrective actions and follow-up.
Many countries have been implementing the Xpert MTB/RIF test for a number of years, with varying
degrees of maturity of individual elements of QA. However, QA activities are often inconsistently
implemented or are not documented. Also, data from QA activities are often not reviewed and used for
decision-making and quality improvement. For example:
• Laboratories are enrolled in an external proficiency testing (PT) programme, but they do not receive
feedback on their performance. As a result, no corrective action is taken in the poorly performing
testing sites and they continue to generate poor-quality results.
• A country has recently implemented standardized training for GeneXpert users, but there is no
participant training log. During supervisory visits, it is reported that many GeneXpert users are not
certified as competent (see Section 4), calling the accuracy and reliability of test results into question.
This guide to operationalizing a QA system can be used by countries to prioritize and plan the
implementation of a QA system to strengthen the quality of their Xpert MTB/RIF testing. The following
parts and sections in this guide describe practical steps for the implementation of a system for ensuring
the quality of Xpert MTB/RIF testing at all levels of the TB diagnostic network.
Part 1: National and Supervisory Levels focuses on establishing or integrating Xpert MTB/RIF
QA activities into the TB diagnostic network in a country or region. This part covers the planning,
implementation and monitoring of Xpert MTB/RIF QA at the central and supervisory levels.
Part 2: QA at Xpert MTB/RIF Testing Sites addresses key activities to be carried out at the testing sites to
ensure the production of quality Xpert MTB/RIF results.
Each part is divided into sections, each dealing with one of the QA elements (Table 1) required for
assuring quality Xpert MTB/RIF test results. Links to additional resources are provided at the end of the
guide. Links to customizable checklists, forms, supporting documents, tools and job aids to assist with
the implementation of QA activities are also provided. These templates can be customized as required.
Part 1: National and
Supervisory Levels
Background
In many countries, implementation of national policies and procedures are coordinated at central level
by the Ministry of Health (MOH), national TB programme (NTP) or national TB reference laboratory
(NTRL). In some settings, particularly in large countries, these activities may be decentralized to the
regional level. Commonly, the coordinating levels provide general guidance and tools for standardized
QA activities. At the regional or district level, supervisory laboratories are responsible for the supervision
of the QA activities and monitoring of the adherence to the procedures in testing sites.
Pillars of a Quality Assurance System
National Planning Procedures & training Testing infrastructure Monitor impact

& supplies
• Governance • Quality procedures • Remote monitoring
• Situational analysis & documentation • Safe & functional site • External quality
• Planning & budgeting • Training & certification • Equipment & supplies assessment (EQA)
• Clinical–laboratory • Data connectivity • M&E
interface
At the national and supervisory levels, the key steps required to develop, implement and monitor a QA
system include:
1. Governance: establish procedures and structures with clearly defined roles, responsibilities, linkages
and focal persons at the national, regional and district levels to plan, implement, manage and monitor
a CQI-based QA system for Xpert MTB/RIF testing.
2. National strategic planning: i) conduct a situational analysis to determine the current quality of
diagnosis using Xpert MTB/RIF and the status of implementation of Xpert MTB/RIF QA activities; ii)
use the data from the situational analysis to design a QA system customized to the country’s situation;
iii) engage private sector and implementing partners; iv) develop a prioritized action plan for phased
implementation of the required QA activities including measuring impact of the plan; v) adequately
budget the activities and set a time line for implementation.
3. Quality procedures and documentation: develop, standardize and disseminate the SOPs, forms,
documents and records that will be needed to ensure the quality of testing.
4. Training and certification: develop and implement a training (initial and refresher training),
competency assessment and certification program to ensure the availability of qualified laboratory
staff.
5. Data connectivity: use remote monitoring systems where possible to collect and analyse data relating
to performance indicators, QA, procurement and supplies management.
6. A safe and functional testing site: assess each testing site for readiness prior to GeneXpert installation
using a standardized checklist and upgrade facilities and procedures as needed to create a safe and
functional working environment.
7. Equipment and supplies
a. Equipment service and maintenance: implement a system to ensure that all GeneXpert
instruments undergo routine maintenance and recalibration according to the manufacturer’s
recommendations.
b. Quality supplies: implement a system to ensure uninterrupted availability of quality-assured
reagents at the testing sites.
8. External quality assessment (EQA): develop and implement an EQA program that includes quality
and performance indicator monitoring, proficiency testing, regular on-site supportive supervision,
and timely feedback, corrective actions and follow-up.
9. Monitor performance of Xpert MTB/RIF testing and of the QA/CQI system: establish an M&E
framework; monitor and evaluate appropriate performance indicators; collect and analyse the data,
using remote monitoring where possible; and use the data for decision making.
10. Clinical-laboratory interface: strengthen the clinical-laboratory interface to ensure that national
testing algorithms are followed, the correct test is ordered for each patient, quality samples are
collected and submitted to the laboratory, accurate results are reported to the clinician, results are
correctly interpreted and patients are promptly placed on appropriate therapy.
Detailed guidance for implementing a functional QA system is provided in the subsequent sections
for each element (however, the order is not meant to be a prescriptive step-by-step one, i.e., complete
element 1 before element 2, etc.). As part of the strategic planning process (Element 2), countries will
prioritize activities and develop a phased implementation plan and time line. Such plans should focus on
providing the appropriate structures (e.g., quality teams, data monitoring units), support (e.g., training,
supportive supervision, constructive feedback) and monitoring and evaluation processes (e.g., collection
and regular analysis of key performance data) needed to implement a functioning CQI process. For
example, implementing a PT program without implementing a corresponding system of timely
feedback, corrective actions and supervisory visits will greatly limit the usefulness and impact of PT on
the quality of testing.
Element 1. Governance
It is important to note that while these guidelines focus

on Xpert MTB/RIF QA programs, governance structures Activities at a glance
already exist for other programs such as HIV, TB, QA
and biosafety of laboratory services. Xpert MTB/RIF
QA activities should be incorporated wherever possible Establish a governance structure
into existing governance structures with clear lines of
communication and reporting. Establish National QA Office
or Coordination team with a
The governance structure at the national and supervisory National Laboratory QA Officer
level will likely vary by country. In many countries, the
central level provides policies, guidance and tools for Establish lines of communication
standardized QA activities, while the regional and district across the diagnostic network
levels operationalize and supervise the QA activities
and monitor adherence to the procedures. In turn, data
collected at the testing sites are reviewed regionally and
centrally and used to inform and update policies and
procedures, thereby closing the CQI cycle (Figure 3).
How do I establish a governance structure?
• Establish a working group on Xpert MTB/RIF QA with appropriate authority and reporting structure
to senior management within MOH to develop or review the governance structure of the Xpert MTB/
RIF QA system
• Assign roles and responsibilities (see Table 2). Develop terms of reference
• Identify the gaps in the capabilities required to perform the assigned roles and responsibilities. As
necessary, develop the needed capabilities
• Develop an organogram of the governance structure that clearly delineates relationships and lines of
supervision
• Establish lines of communication and reporting within the governance structure. Map out the flow of
information and identify points of contact
Figure 3: Continuous quality improvement cycle
Supervision & Guidance
MOH / NTP / NTRL

Central Level
XPERT MTB/RIF QA PROGRAMME
DATA
Regional Level
Supervision & Guidance
DATA DATA
Site Level
Table 2. Example of a governance structure with defined roles and responsibilities
Entity Roles and responsibilities
• Establish the CQI strategy, vision and mission

• Establish a National QA office or Coordination team and appoint a National Laboratory QA
Officer who works closely with the National Clinical Services QA Officer
• Engage implementing partners and private sector in QA processes
• Establish Laboratory Technical Working Group (TWG) to assist in the formulation and
implementation of national policies and procedures
MOH • Oversee a process to develop Xpert MTB/RIF EQA policies and procedures
• Oversee a strategic planning process that includes
– a situational analysis
– design of a QA system customized to the country’s situation
– development of a costed, prioritized action plan for phased implementation with targets
and time line
• Allocate an adequate budget for QA activities
• Ministry of Education: ensure that CQI and QA knowledge forms part of the core
curriculum of academic and training institutions and part of the scopes of practice of
Other Ministries relevant healthcare professionals as appropriate (laboratory, doctors, clinical officers, nurses,
programme managers, etc.) in collaboration with the relevant statutory Professional Councils
• Ministry of Finance: manage financial issues related to laboratory programs
• Develop and implement the National Strategic Plan for TB Control (NSP)
• Oversee the TB diagnostic network
• Participate in the development of Xpert MTB/RIF QA policies and procedures
NTP • Enforce TB QA policies and procedures throughout the TB diagnostic network, in particular
focusing on pre- and post-analytical processes
• Provide training, guidance and technical assistance
• Oversee monitoring and evaluation programmes
• Provide technical input for the development of Xpert MTB/RIF QA policies and procedures
• Enforce TB QA policies and procedures throughout the TB laboratory network
• Provide guidance and technical assistance
• Develop, standardize and distribute the SOPs, forms, documents and records needed to
ensure the quality of testing
• Develop, implement and manage systems to:
– train, assess competency and certify laboratory workers for Xpert MTB/RIF testing
NTRL – ensure that all GeneXpert instruments undergo routine maintenance and recalibration
according to the manufacturer’s recommendations
– ensure uninterrupted availability of quality-assured reagents at the testing sites
– remotely collect and analyse data relating to performance indicators, QA and procurement
• Coordinate the QA activities and provide samples for proficiency testing
• Supervise and manage regional and district facilities responsible for supervising testing sites
• Establish an M&E framework; monitor and evaluate performance and quality indicators;
collect and analyse the data; and use the data for decision making
• Enforce TB QA policies and procedures in the testing sites

Regional • Conduct supervisory visits of testing sites and provide supportive supervision
and district • Evaluate QA indicators, provide timely feedback, recommend corrective actions and follow-
supervisory up on corrective actions
laboratories • Provide training, guidance and technical assistance to testing sites
• Collect and compile data on performance and quality indicators and report to central level
• Ensure accountability, leadership and governance at health facility level

Health Facility
• Provide oversight and coordination for QA and CQI activities at the institution
Quality
• Provide regular progress reports to the regional QA structure
Committee
• Translate policy into practice
10
Element 2. Strategic planning
The strategic planning process should include 1) a

situational analysis to determine the current status of Activities at a glance
Xpert MTB/RIF QA activities; 2) design of a QA system
customized to the country’s situation; 3) development of a
costed prioritized action plan for phased implementation Assemble the team
of the required QA activities with targets and a time line;
and 4) allocation of an adequate budget and resources for Define roles and responsibilities
the implementation and annual operation of QA activities.
Conduct situational analysis
What you need to do
Develop a strategic plan to
2.1. Understanding the current quality of the implement and sustain the QA
Xpert MTB/RIF testing network system
A situational analysis should be conducted in order to i) Set the budget and time line
determine which Xpert MTB/RIF QA activities are being
implemented at central, supervisory site and testing site
levels, ii) measure their impact on testing quality and iii)
identify the gaps in providing quality assured Xpert MTB/RIF results. A situational analysis should be
conducted as an initial step in developing or revising a QA system and periodically (e.g., every 3 to 5
years) thereafter to evaluate progress.
A strong commitment from the MOH and implementing partners is essential if QA activities are to
be successfully implemented. The activities must align with applicable existing national, regional, and
testing site priorities. The MOH/NTP/NTRL should delegate the responsibility for conducting the
situational analysis and planning of the Xpert MTB/RIF QA activities to a team led by a suitably
qualified individual.
Who should lead the situational analysis?
• The QA focal person should coordinate the situational analysis, in collaboration with an implementing
partner where needed, this may be the National Laboratory QA Officer, GeneXpert focal person, NTRL
Quality Officer or other delegated individual or team identified by MOH/NTP/NTRL.
How do I select the team?
• Assemble a team that includes representatives of:

a. MOH (laboratory and clinical services)
b. NTRL
c. Xpert MTB/RIF implementing partners
d. Testing site managers
e. Data analytics
• Make a list of stakeholders to be consulted during the process. These should include:
a. Programme managers
b. Regulatory bodies
c. Private sector
d. Clinical staff
e. Other local experts, such as implementing partners
• Identify key individuals who may contribute to establishing or integrating the QA activities
• Set up a meeting with the key stakeholders. Consider using existing meeting structures (e.g., MOH
quarterly meetings) to engage individuals
• Introduce the QA activities and QA system to the key stakeholders
• Determine stakeholder willingness to participate in the QA team
11
What does the team do?
• Coordinate, conduct and report results of a situational analysis

• Advise MOH/NTP/NTRL on strategies to implement Xpert MTB/RIF QA activities
• Develop action plans that ensure all aspects of quality are met
• Oversee the rollout of the QA activities
• Assess the impact and scale-up of the Xpert MTB/RIF QA activities
How do I plan the situational analysis?
• Use the Situational Analysis Checklist and Xpert MTB/RIF Continuous Quality Improvement (Xpert
CQI) Assessment Checklist for Testing Sites (ACTS)
• Arrange a planning meeting to review the checklists
• Select the testing sites to be included in the analysis (see the box below)
• Assign a timeframe for conducting the assessment
• Assign responsibilities to stakeholders
• Provide the necessary data collection tools and sensitize all stakeholders responsible for data collection
on the checklist and means for data verification
• Supply stakeholders with a list of documents (e.g., policies, reports, forms, etc.) that need to be
collected as part of the assessment
• Designate the responsibility to compile the situational analysis report to members of the Technical
Working Group, sub-group or other designated persons
How do I select the testing sites?
• Divide the country districts into areas defined by difficulty to access, geography, epidemiologic
situation or other criteria
• Randomly select one district per area
• Select all the testing site(s) located in the identified districts for analysis(consider sampling if there are
a large number of sites in any selected districts)
• To assess the entire diagnostic network, include (even if they are not contained in the
selected districts):
–– facilities at different levels of the health system
–– private sector facilities
–– at least one testing site from each major implementing partner
–– facilities that refer and receive specimens
–– non-laboratory point-of-care testing sites
What should be included in the situational analysis report?
• Introduction and objective: State why Xpert MTB/RIF QA activities are needed and define activity
objectives
• Situational analysis: State the need for the situational analysis; explain how the situational analysis was
conducted; and describe who and what was assessed
• Findings: Report the findings of the situational analysis. Consider organizing the findings according to
the key steps in the roadmap for the national and supervisory levels and for the testing site
• Recommendations: Outline the problems that were identified during the situational analysis, how and
by whom they may be addressed and provide a time line for resolution. Budget: Include a detailed
budget for the proposed activities and the resources required to address the identified gaps and
implement recommendations
12
The situational analysis report should describe gaps identified, recommendations for how to implement
QA activities and propose a time line for implementation based on the current level of implementation
(e.g., some testing sites will already have implemented a high proportion of recommended activities
while others have not). Recommendations should address gaps at the national and supervisory levels
and at the testing site level. The report should be reviewed and endorsed by the Xpert MTB/RIF
Technical Working Group (TWG) before presenting the report to senior management at MOH/NTP.
An excerpt from an example situational analysis checklist with commonly observed outcomes and
recommendations, can be found in the Supporting documents/forms and templates9.
Based on the country governance structure, the responsibility for prioritizing implementation of
the report recommendations and developing an operational plan may be at national level or may be
delegated to the regional level. In any case, priorities should be agreed at national level by the TWG
and this body should receive regular updates on progress towards implementation (see Element 9).
It is important to include implementing partners and all stakeholders involved in implementation,
particularly with respect to mobilization of resources and technical assistance.
2.2. Prioritize interventions
The outcome of a situational analysis informs the implementation of QA activities at the central,
regional, testing site and clinical site level. Some activities might or might not have already been
implemented, some with and without QA components. The phased implementation plan and time line
should focus on providing the appropriate structures (e.g., quality teams, data monitoring units), support
(e.g., training, supportive supervision, constructive feedback) and monitoring and evaluation processes
(e.g., collection and regular analysis of key performance data) needed to implement a functioning QA
process. For example, implementing a PT program without implementing a corresponding system of
timely feedback, corrective actions and supervisory visits will greatly limit the usefulness and impact of
the PT program on the quality of testing.
Depending on the nature of a QA activity, it may be implemented simultaneously at all testing sites (e.g.,
establishing a national PT programme) or may rely on individual site level implementation (such as
conducting routine maintenance tasks), and therefore the progress will depend on site level motivation,
capacity and resources. Monitoring of indicators at a national level will highlight such differences and
should help in addressing challenges in implementation, and in learning from best practices in well-
performing sites or regions.
Depending on available human resources and funding, countries may decide to prioritize
implementation of certain activities that could rapidly produce improvements in the quality of
testing with a limited investment. That is, certain activities require limited resources, beyond initial
development of data collection tools and training of staff. Others may require national level action
and decisions, such as development and availability of national training curricula and recording and
reporting forms. As such, individual sites may rely on higher level input in order to meet these criteria.
Countries may focus on implementation of all QA components and monitoring of all indicators at a
selected number of sites initially, and once successfully implemented, go on to develop a plan for scale-
up to all sites. Alternatively, countries may work on establishing a selection of QA activities at all sites,
then expanding the range of QA activities once the initial implementation has been completed. Either
way, an important focus should be on clinical and programmatic indicators and process indicators, and
not just on laboratory performance indicators.
9 The example contains excerpts from a situational analysis checklist, and is not fully inclusive. The situational analysis checklist must be used to
provide a comprehensive overview of Xpert MTB/RIF quality assurance activities.
13
2.3. Set the budget and time line
Successful implementation of QA activities for the Xpert MTB/RIF test will require financial
commitment from MOH and NTP and the testing sites, with support of the implementing partners.
In some countries, funding will also be allocated by state or regional governments and by institutions.
A budget should be developed to address both the implementation of recommendations from the
situational analysis and the implementation and sustainability of the QA activities thereafter.
A GeneXpert costing tool is available on the FIND website:
https://www.finddx.org/implementation-resources/#tb
Table 3: Budgetary considerations for QA activities
QA activity Budgetary considerations
• Preparation & printing of standardized test request & results reporting forms
Generate QA • Preparation & printing of standardized logbooks
documentation • Regular review of all Xpert MTB/RIF documents (SOPs, checklists, etc.) based on
national requirements
Remote monitoring • Costs associated with providing a remote monitoring system in-country
Maintain & service

• Site upgrades, calibration kits and warranty costs
equipment
• Material cost per test, including but not limited to Xpert MTB/RIF test reagents,
Strengthen the supply
consumables, sample collection items, printing paper, etc. Additional equipment
chain
costs, such as printer, computer, printer cartridges, shipping & courier costs
• Preparation of training materials for each of the QA activities:

– Training of Trainers (TOT)
– Training of GeneXpert users & advanced users
Conduct training,
• Costs associated with facility and classroom-based training including travel,
competency testing &
accommodation, printing materials, venue hire & catering. Personnel wages are
certification
excluded, as these are not expected to add additional costs to the activity
• Costs of competency testing
• Costs of refresher trainings and trainings of test updates
• Preparation of checklists for supervision and troubleshooting

Conduct onsite
• Site visits (including printing checklists, travel to sites, daily subsistence allowance
supervisory visits
for visits to remotely located sites)
• Costs associated with management of externally produced panels: consider

distribution of panels, analysis of reports, visits to participating sites
• Costs associated with providing PT panels produced in-country. Costs do not
include human resource and laboratory setup costs:
– Determine the capacity that exist in-country to manufacture panels
– Map out financial resources that will be required: consider preparation,
Implement PT testing
dissemination, collection, analysis and reporting of data, visits to sites participating
in PT
– Include costs associated with establishing the capacity in country including any
needed trainings, technical assistance
– Include costs associated with external quality assurance and internal quality control
of the PT panels
14
Element 3. Quality procedures and documentation
Without accurate and complete documentation, the quality

of Xpert MTB/RIF test results may be compromised. The Activities at a glance
documentation must address activities throughout the
diagnostic cascade including documentation for clinical
activities (e.g., specimen collection and referral) and Generate QA documents
laboratory activities.
Disseminate QA documents
Standardized documents and forms should be developed
at the national level and distributed to all testing sites in Implement a document
order to assure conformity control system
Standardization of documents and forms will take time.

Therefore, plan the implementation of standardized
documentation in a systematic manner.
SOPs, forms and other documents must be up-to-date, accurate and readily accessible at all testing and
participating clinical sites.
A document control system is needed to ensure regular review of quality management documents (e.g.,
SOPs) and to ensure the correctness of the documentation that supports laboratory testing.
How do I generate QA-related documentation?
• Review the list of required documents (see above)

• Review the situational analysis - what needs to be written/revised/ standardized?
• Assign writing and review responsibilities
• Review the revised documents for approval
• Provide training in the use of the documents
• Disseminate to the testing sites
• Review documentation implementation during supervisory visits
How do I create a document control system?
• Write an SOP for Document Control including the Document Retention List
• Create a Document Retention List: determine storage time and location for all types of
documents used
• Make a Document Control Log
• Design a Document Revision Form
• Add a front page to each quality document used in the laboratory to track versions
• Create folders for storing SOPs at the most convenient locations (at the testing site) for staff to have
access to the SOPs when needed
• Develop personnel files for all staff members to document their knowledge of the correct documents
• Provide training and roll out the document control system
15
Table 4: SOPs, forms, and other documents that must be available at all testing sites
Resource Description
Describes a step-by-step protocol for diagnosis of TB at

National TB Diagnostic Algorithm
healthcare facilities
Document Control SOP Describes the procedures to ensure that the correct
http://www.gliquality.org/activities/2/33 documentation (e.g., SOP) is used for laboratory testing
Describes the procedures to be followed to ensure

Specimen Collection & Transport SOP
collection of good quality specimens & safe, rapid
transport of specimens to the testing site
Test Requisition Form Form for requesting Xpert MTB/RIF testing
Register for recording patient, specimen, & test

Laboratory Register
information
Describes a procedure for specimen referral & provides

Specimen Referral SOP & forms
the necessary forms
Xpert MTB/RIF test SOP Describes the procedures for performing the Xpert
https://www.finddx.org/implementation-resources/#tb MTB/RIF test
Describes the procedures for performing the Xpert

Xpert MTB/RIF Ultra test SOP 10
MTB/RIF Ultra test
Describes the general principles and procedure for

Proficiency Testing (PT) SOP testing PT samples, resulting, reporting, and corrective
action for unacceptable results
GeneXpert maintenance log Form for recording GeneXpert maintenance tasks
Temperature monitoring records Form for recording daily temperature monitoring in

https://www.finddx.org/implementation-resources/#tb testing and kit storage areas
Non-conformity & corrective action log Form for capturing non-conformities and corrective
https://www.finddx.org/implementation-resources/#tb actions
Describes the procedure of safely disposing

Waste management SOP
consumables and Xpert MTB/RIF reagents (may be
included in a Biosafety SOP)
Describes the procedure to follow in the event of a

Spill management SOP
biohazard spill at a testing site (may be included in a
Biosafety SOP)
Xpert MTB/RIF WHO reporting codes Describes the standard WHO reporting codes for
http://www.who.int/tb/publications/definitions/en/ reporting Xpert MTB/RIF test results
Form for capturing Xpert MTB/RIF performance

Xpert MTB/RIF performance indicator reporting form
indicator data
Xpert MTB/RIF test reporting form Form for reporting Xpert MTB/RIF test results to
http://www.who.int/tb/publications/definitions/en/ clinicians
Form for documenting the results of the investigation

PT failure investigation and corrective action form
of PT failures and remedial action taken
10 Xpert MTB/RIF and Xpert MTB/RIF Ultra package inserts can be requested from: http://www.cepheid.com/en/support/package-inserts-uk/pack-
age-insert-entry-form
16
Element 4: Training, competency assessment and certification
Training, competency assessment and certification are

critical components of providing quality assured Xpert Activities at a glance
MTB/RIF test results. The implementation of the Xpert
MTB/RIF test in a quality assured manner requires
training beyond the steps required to carry out the Customize training package
test. Manufacturer-supplied, on-site training following
installation is often too short to cover QA activities. Conduct training
The testing site manager must ensure that users receive
adequate training in QA and other key aspects of testing. Perform competency
assessments
To date, most countries have relied upon national
trainings, which have generated well-trained users and
advanced users. However, testing sites have found that
this system does not always guarantee sufficient numbers of GeneXpert users. In some settings, national
training is not offered frequently enough or trained users may be lost due to staff attrition, both
situations leading to inadequate testing coverage. One proven solution is to develop capacity of testing
sites to conduct training and competency assessment of their staff using nationally developed guidelines
and training materials. The evolving role of the national level is to develop national training curriculum,
to provide implementation guidance, and to monitor training and competency assessment activities.
What you need to do
4.1 Develop a national training curriculum for the Xpert MTB/RIF test
• The training programme should be standardized by the MOH/NTP and include training curricula for
trainers, users and advanced users. A significant portion of the training should be devoted to hands-on
training that incorporates quality assurance elements.
• All training (whether at national or site level) should use a single nationally developed curriculum.
• Training of clinical healthcare workers is also critical in ensuring quality Xpert MTB/RIF test results.
Clinical healthcare workers must understand how to interpret Xpert MTB/RIF test results, as well as
the limitations of the test (http://www.stoptb.org/wg/gli/TrainingPackage_XPERT_MTB_RIF_Ultra.asp).
• Training should be provided for programme and laboratory managers and their implementation
partners on key topics for diagnostic network strengthening including implementing a QA system
(http://www.stoptb.org/wg/gli/TrainingPackage_Programme.asp).
• A Training-of-Trainers (TOT) approach should be used to establish and sustain a team of competent
local trainers and mentors. Competency of trainers and mentors should also be assessed by master
trainers and mentoring provided over time to develop all necessary skills required to independently
manage the programme.
–– The GLI training package contains modules (Table 5) that can be customized and adapted to
include country-specific elements
–– GeneXpert Users: Modules are selected and customized to provide testing site personnel
with the skills and knowledge to perform the Xpert MTB/RIF test, understand the testing
algorithms, interpret Xpert MTB/RIF test results, maintain the GeneXpert instrument, perform
quality assurance procedures, and supply the NTP with relevant performance indicators.
–– Module 12 of the GLI training package: It is dedicated to QA of the Xpert MTB/RIF test. This
module needs customization once country-specific performance indicators and documentation
have been identified.
–– GeneXpert Advanced Users: Modules are selected and customized to provide advanced
users with the skills to co-ordinate Xpert MTB/RIF test implementation activities, such as
supervisory visits, competency assessments and troubleshooting in their regions.
17
• Criteria for competency should be agreed and documented, and only training participants who meet
the criteria should be certified as competent.
• Certificates should be issued to competent users and training reports provided to MOH/NTP for all
trainings.
• All implementing partners should use the National Training Curriculum for the Xpert MTB/RIF test
for training users.
• A register of certified users and advanced users should be kept by MOH/NTP.
• Criteria for retraining at regular intervals and for personnel who do not pass the initial assessment
should be determined.
How do I develop a training and certification programme for Xpert MTB/RIF?
• Review the situational analysis to determine how many trainers (or potential trainers) are available
compared with country need for training
• Review the situational analysis to determine the number, level and location of users who need training
• Review GLI training materials and develop or revise training materials. Have training materials
reviewed and approved by MOH
• Develop a register of certified users, advanced users and trainers and assign responsibility for
managing register
• Conduct a TOT. Consider using local or international trainers from implementing partners if there is
no in-country expertise to conduct the training
• Conduct GeneXpert user trainings and competency assessments. Consider using centralized trainings
or training on testing sites
• Identify potential advanced users from the cadre of trained GeneXpert users
• Conduct advanced user training and competency assessments
• Deploy the advanced users to introduce regular competency assessments at testing sites
• Review training records and participants’ performance during supervisory visits and conduct refresher
training where needed
In situations where nationally conducted Xpert user’s training is not sustainable, a standardized training
curriculum for training of users at the testing sites may be developed. Onsite training may be conducted
by trained users with documented competency level 4 or 5 and by supervisors during supportive
supervisory visits at the testing sites. A standardized, approved training checklist should be used to
document training and to ensure all technical and QA activities were included.
4.2. Perform competency assessments
• Competency assessments should be performed after training and periodically thereafter (e.g.,
annually). Competency assessment should include assessment of skills for performing on-site
supervision, training and mentoring as well as performing the test. Templates for recording the
results of a competency assessment for a GeneXpert user and an advanced user are available in the
Supporting Documents/forms and templates.
18
Table 5: Available training packages
Contents of the GLI training package for Xpert MTB/RIF (Ultra)
Module 1 TB Biosafety
Module 2 Specimen Collection & Referral
Module 3 Procurement & Inventory Management
Module 4 Recording & Reporting Results
Module 5 Monitoring Quality Indicators
Module 6 Quality Assurance of the Xpert MTB/RIF (Ultra)
Module 7 External Quality Assurance
Module 8 Clinical Guide to Xpert MTB/RIF (Ultra)
http://www.stoptb.org/wg/gli/TrainingPackage_XPERT_MTB_RIF_Ultra.asp
Contents of GLI training package: Programme modules for diagnostic network strengthening
Module 1 TB Diagnostics: Global Policies and Strategies
Module 2 Implementing TB Diagnostics: Practical Considerations
Module 3 Plan and Establish a Sample Referral Network for TB Diagnosis
Module 4 Plan and Implement a Quality Assurance Programme
Module 5 Plan and Implement Connectivity Solutions
Module 6 Monitor and Evaluate Your Programme
Module 7 Funding Your Programme
Module 8 Plan an Integrated Diagnostic Approach
http://www.stoptb.org/wg/gli/TrainingPackage_XPERT_MTB_RIF_Ultra.asp
19
Element 5. Data connectivity and remote monitoring
Diagnostics connectivity refers to the ability to connect

diagnostic test devices that produce results in a digital Activities at a glance
format, such as GeneXpert instruments, in such a way as
to transmit data rapidly and reliably to a variety of users.
Key features of the systems are the ability to remotely Select a data connectivity
monitoring performance, conduct QA and manage solution
inventory. With remote monitoring, designated persons
can use any internet-enabled computer to access the Connect all GeneXpert
software platform, providing them with an overview of instruments
the facilities, devices and commodities in their network.
For example, the head of a supervisory laboratory or Prepare SOPs and train users
other authority can easily see how many tests are being
performed and where; what are the results; and which sites
are underperforming or experiencing abnormal results or
errors, which may highlight a need for troubleshooting, device repairs, targeted on-site supervision, or
retraining of technicians. Software can track consumption and inventory to avoid stock outs and expiring
cartridges as well as potentially identify commodity lots or specific instruments with poor performance
and abnormal error rates for QA purposes and can provide a highly cost-effective way to ensure proper
functioning of a diagnostic device network.
Data can also be transmitted automatically to 1) clinicians and patients which allows for faster patient
follow-up, 2) laboratory information management systems or electronic registers, reducing staff time
and the chance of transcription errors, and greatly facilitating monitoring and evaluation processes and
3) the NTP to assist with surveillance of trends on disease or resistance patterns as well as enhance the
capacity of NTPs to generate performance indicators and to provide the data needed for several of the
top 10 indicators of the End TB Strategy. Because of the promise to improve recording, reporting and
monitoring of data and performance indicators, diagnostics connectivity has been incorporated into two
of the indicators for laboratory strengthening under the End TB Strategy:
• Indicator 4: all sites that use WHO-recommended rapid diagnostics should be transmitting results
electronically to clinicians and to information management systems using data connectivity solutions
no later than 2020
• Indicator 9: remote monitoring via data connectivity solutions should be used to monitor key
performance indicators at all sites that use WHO-recommended rapid diagnostics no later than 2020
20
Diagnostics connectivity solutions, especially for Xpert MTB/RIF testing, are the way of the future.
Countries should give high priority to investing in developing and maintaining such systems and
in training personnel to operate them and to use the data generated for decision making. Detailed
information on the design and implementation of a diagnostics connectivity solution may be found in
the GLI Quick Guide to TB Diagnostics Connectivity Solutions.11
• Assist with surveillance • Near real-time consumption

of trends on disease or based forecasting
resistance patterns • Monitor stock expiration
• Monitor warranties
Surveillance Supply chain
Monitor quality Recording and

• Remote monitoring of
indicators reporting
performance
• Facilitates data collection • Reduces clerical errors
and reporting of quality • Speeds up reporting to
indicators clinicians
Diagnostics connectivity solutions typically comprise: 1) a connectable diagnostic device that produces
electronic data, 2) a software platform that receives and interpret and displays data and 3) a means to
transmit data from the device to the software platform and to a server. Systems have been developed
by Cepheid, USA (C360), SystemOne (GxAlert™/Aspect™), Savics (DataToCare™) and Blue Frontier
(Connected Diagnostics Platform). See TB Connectivity Solutions for a comparison of the available
systems. Importantly, the developers are collaborating to ensure the compatibility of the systems. The
systems connect GeneXpert instruments to central in-country servers or cloud-based servers via the
internet or short message service (SMS). Instrument data can be accessed via web-based dashboards. The
software can usually be configured so that subsets of data can be securely made available to those who
need access to it. Security protocols also protect the privacy of the patient.
However, remote monitoring systems only help with collection of instrument-related data, and systems
need to be put in place to collect and review other data, as described above. Nonetheless, they can greatly
simplify and improve speed and quality of test data collection and access to automated reports at testing
site, regional or national level.
11 GLI Quick Guide to TB Diagnostics Connectivity Solutions. 2016. http://www.stoptb.org/wg/gli/gat.asp
21
How do I select a data connectivity solution?
• Conduct an in-country assessment of existing systems and infrastructure (both laboratory and
connectivity). Technical assistance from a diagnostics connectivity expert may be needed. Key
considerations include:
–– Is on-site internet service or 2G/3G cellular services available and sufficiently stable for the
remote monitoring system?
–– What hardware and software will need to be installed and maintained at the testing site?
–– Who will have access to the data?
–– What training will be required for testing site staff to access the system? How will data
be secured?
–– How, and at what frequency, is the system backed-up?
–– What are the associated costs of implementing and maintaining a remote monitoring system
(e.g., internet access charges, information technology support, software licenses)?
• Based on the assessment, develop recommendations for the planned diagnostic connectivity solution
and data needs
• Develop a costed roadmap
• Develop and operational budget that provides for:
–– Project management, data monitoring and supervision costs
–– Remote or in-country technical support, IT-support and updates, costs
–– Running costs for connectivity, e.g., monthly mobile data costs, server hosting, etc.
How do I connect all GeneXpert instruments?
• Determine if an internet-based or cellular systems-based solution will be used

• Install all needed hardware and equipment at each site, e.g., routers, modems, server, or SIM cards and
establish maintenance plans
• Set up the connectivity solution at each site, technical assistance from the diagnostics connectivity
solutions provider may be needed
• Establish units at the national, regional and local level to systematically monitor data on a weekly or
biweekly basis
• Develop SOPs for access, reporting, data entry, data security and data back-up
How do I train users?
• Conduct implementation workshops and trainings that include data collection, data use and
management and day-to-day operations of connectivity solution
• Provide initial training for new users and refresher training for existing users as needed
How do I monitor and evaluate a diagnostics connectivity system?
• Develop or adopt objectives, outcome measures, impact indicators, process indicators and
performance indicators for the diagnostics connectivity systems
• Routinely collect and analyze the data to inform connectivity management and inform policy
22
Element 6. A safe and functional testing site
Failure to provide a safe and functional work environment

can impact the quality of testing in several ways including: Activities at a glance
• An unsafe testing site is a hazard to staff, patients and the

environment Assess each testing site for
• In an unsecure testing site, test results may be delayed if readiness
there is equipment failure or theft
• Testing sites that do not maintain uninterrupted power, Upgrade facilities as needed to
optimal working temperature and a clean environment create a safe functional work
can have equipment failures and high error rates that environment
delay reporting and waste reagents
Regularly assess existing testing
The selection of which sites will conduct Xpert MTB/ sites for safety and functionality
RIF is usually directed by the NTP or NTRL and is based
on factors such as the testing workload, the efficiency of
referral networks and patient access to services. The Xpert
MTB/RIF testing sites may be located in a peripheral clinic, district laboratory, or a high-throughput
reference laboratory.
In addition to evaluating new sites, existing testing sites should also be regularly assessed for providing a
safe and functional testing site using a standardized checklist.
What you need to do
As part of the QA process, each testing site should be evaluated for readiness using a standardized
checklist12 prior to the installation of the GeneXpert instrument and any testing of clinical specimens.
Key infrastructure requirements are:
• a stable and continuous electrical supply

• an uninterrupted power supply (UPS) that will last a minimum of two hours to allow completion of
a run
• an ambient temperature of 15–30°C in the room where the instrument is used (humidity control may
also be needed)
• a clean environment with little dust
• adequate storage space for the cartridges with a consistent temperature of 2–28°C, monitored daily
• security to protect against theft of the instrument or computer
• adequate ventilation to meet WHO biosafety requirements
–– when appropriate microbiological techniques are used, processing of specimens for the Xpert
MTB/RIF assay may be carried out on an open bench in an adequately ventilated area.
–– when the climate or use of air conditioning prevents the use of natural ventilation (e.g., from
open windows), mechanical ventilation systems may be needed to provide an inward flow of
air without recirculation in the room or the use of ventilated workstations or certified biosafety
cabinets may be needed to ensure a safe working environment.
• appropriate facilities and equipment (e.g., autoclaves or incinerators) to safely dispose of
biohazardous waste
12 Xpert pre-installation checklist. https://www.finddx.org/wp-content/uploads/2016/03/Pre-installation-checklist_10-2014.pdf
23
Similarly, the sites should be assessed to determine if all the required policies and procedures (e.g., SOPs
for waste disposal) for safely conducting the Xpert MTB/RIF test are in place.
If the Xpert MTB/RIF testing site does not meet the infrastructure requirements, the national and
supervisory levels should work with the testing sites to upgrade facilities and procedures to create a safe
and functional working environment.
How do I create a safe and functional testing site?
• Have an experienced assessor evaluate the readiness of each testing site using the Xpert
pre-installation checklist (https://www.finddx.org/wp-content/uploads/2016/03/Pre-installation-
checklist_10-2014.pdf)
• Pay particular attention to the required electrical supply, ambient and storage conditions, physical
security, biosafety and waste disposal
• As necessary, work with the facilities to upgrade infrastructure and procedures and provide training in
safe working practices
• Regularly assess existing sites by an experienced assessor using the Assessment Checklist for Testing
Sites (ACTS). This may be done as part of a supervisory visit
24
Element 7. Equipment and supplies
The GeneXpert is a precision instrument that requires

regular maintenance to ensure that it provides accurate Activities at a glance
and precise results. A robust inventory system is required
to monitor Xpert MTB/RIF cartridge consumption.
Accurately forecasting the Xpert MTB/RIF test supply Develop and implement plans
needs reduces the risk of an interruption in service due to ensure maintenance and
to shortage of reagents. Failure to maintain an adequate, servicing of the GeneXpert
uninterrupted supply of quality-assured reagents can affect instrument
quality because 1) stock-outs result in delayed testing and
delayed reporting of results and 2) use of poor quality Establish a system to ensure an
or expired reagents can result in high error rates and uninterrupted supply of quality-
inaccurate test results. assured reagents
What you need to do Implement a system for new lot

testing of batches of cartridges
7.1. Equipment service and maintenance
Without regular maintenance and servicing, the GeneXpert

instrument cannot generate accurate and reliable Xpert MTB/RIF test results:
• All GeneXpert instruments must be evaluated as being “fit for purpose” through verification with
known positive and/or negative material prior to commencing testing of clinical specimens. Instrument
verification is conducted at installation, after service or calibration, or after moving instruments.
• All GeneXpert instruments must undergo routine maintenance and recalibration according to the
manufacturer’s recommendations.
• Basic preventative maintenance should be carried out daily and weekly by users at the test site and
some advanced maintenance can be done by superusers during supervisory visits.
• Servicing and repair of instruments should be carried out by authorized service providers.
Detailed guidance for equipment maintenance can be found in the Tuberculosis Laboratory
Maintenance Plan (LMP) for Preventive and Routine Maintenance of Laboratory Equipment13
developed by the European TB Laboratory Initiative.
Remote monitoring systems can identify specific instruments or modules with poor performance or
high error rates which indicate a need for service or repair. Also, some remote monitoring systems track
the status of warranties as well as the status of the calibration of instruments and alert users to schedule
renewal of maintenance agreements or recalibration service.
How do I ensure well-functioning GeneXpert instruments?
• Ensure that all GeneXpert instruments are evaluated as being “fit for purpose” at installation, after
service or calibration, or after moving instruments
• Ensure that all GeneXpert instruments undergo routine maintenance are according to the
recommended daily, weekly and monthly schedules. Records of maintenance must be kept and
reviewed at least monthly by the testing site manager and during supportive supervisory visits
• Ensure that all GeneXpert instruments are recalibrated according to the manufacturer’s
recommendations. Monitor recalibration schedules at the national or supervisory levels
• Use remote monitoring capabilities to monitor the performance of GeneXpert instruments and
individual modules
• Obtain servicing and repair of instruments from authorized providers. Develop a national SOP for
obtaining service
• Purchase extended warranties or service contracts for each GeneXpert instrument
13 Tuberculosis Laboratory Maintenance Plan (LMP) for preventive and routine maintenance of laboratory equipment. European TB Laboratory
Initiative. 2017. Available at http://www.euro.who.int/__data/assets/pdf_file/0009/355788/WHO-ELI-TB-Lab-Maintenance-Plan_ENG.PDF
25
7.2 Quality supplies
The quality of the Xpert MTB/RIF testing service depends on the uninterrupted availability of quality-
assured reagents at the testing sites.
7.2.1. Strengthen the supply chain
Distribution of Xpert MTB/RIF test reagents to testing sites requires special consideration, as the
reagents have a limited shelf life and temperature-controlled storage requirements. The testing site
performance indicators are used to calculate consumption rates. The regular TB supply chain should be
used for distribution of reagents; however, due to transport issues, it may be necessary to implement a
district-level stock buffer to ensure stock-outs do not occur.
Effective supply chain management is a complex process that includes product specification, product
selection, forecasting of needs, procurement, distribution and storage and use. Managing a laboratory’s
commodities involves careful planning and coordination and should follow the well-recognized cycles
of selection, procurement, distribution, and use. General guidance can be obtained from various sources,
including USAID/Deliver: Guidelines for Managing the Laboratory Supply Chain14.
Remote monitoring systems can facilitate inventory management, by allowing stocks to be entered at
site-level and forecasting the anticipated stock-out date or potential expiring cartridges based on the
consumption rate. Replenishment of inventory can be managed before stock out, or potential expiring
cartridges can be prioritized or moved to other sites. In addition, the tracking of lot numbers can
identify poor performance and abnormal error rates for quality assurance purposes.
7.2.2. New lot testing
New lot testing, also known as lot-to-lot verification, should be performed on new batches of cartridges.
New lot testing usually consists of testing a sample of the new cartridges and comparing the results to
existing lot of cartridges with known performance. A new lot testing example SOP is available in the
Supporting Documents/forms and templates.
• Conditions during transport & storage of cartridges may affect their performance.
• Cartridge test failures could indicate that the new batch of cartridges is not fit for use.
• New lot testing is preferably performed at the central level (e.g., NTRL), thereby ensuring that cartridges
with test failures are not distributed, and reducing the burden of testing and number of cartridges used.
New lot testing at regional or testing site level monitors conditions during transport and storage of
cartridges in-country.
How do I ensure the quantity and quality of supplies?
• Develop and implement a system to ensure an uninterrupted supply of quality-assured reagents

• Establish a system for monitoring inventories and forecasting supply needs
• Use remote monitoring capabilities to monitor consumption of supplies, demand for supplies,
inventories and expiry dates of cartridges.
• Have a mechanism in place to reallocate supplies to avoid shortages and expiration of cartridges
• Conduct new lot testing on each new batch of cartridges (at least at the national level)
14 Guidelines for Managing the Laboratory Supply Chain: Version 2. USAID | DELIVER PROJECT, Task Order 1 2008. http://deliver.jsi.com/dlvr_con-
tent/resources/allpubs/guidelines/GuidManaLabSC_v2.pdf
26
8. External quality assessment (EQA)
An EQA program includes quality and performance

indicator monitoring, proficiency testing (PT), regular Activities at a glance
on-site supportive supervision, timely feedback, corrective
actions and follow-up. On-site supervision should be
prioritized to poorly performing sites as identified during Develop and implement a
proficiency testing, monthly monitoring of performance program for on-site supervision
indicators or after site assessments. prioritizing poorly performing
sites
8.1. On-site supervision
Develop and implement a
On-site supervisory visits for assessment and training are proficiency testing program
especially critical during early stages of implementing
a new test or procedure as they provide motivation and
support to staff, especially in peripheral settings. On-site
supervisory visits are also good opportunities to provide refresher training, mentoring, troubleshooting
advice and technical updates. Strong relationships with GeneXpert users encourage rapid reporting
of any problems and enable rapid troubleshooting, re-training and corrective actions. On-site
supervisory assessments should be documented using standardized checklists to ensure consistency and
completeness of information and to enable monitoring of trends and follow-up on recommendations
and corrective actions. An on-site supervisory programme requires substantial planning and resources
(both financial and human).
Develop and implement a program for on-site supervision
• Developing the program

–– Adequate numbers of trained staff and funds must be available for on-site supervisory visits
and assessments.
–– On-site supervisory visits should be planned at regular intervals with schedules communicated
to sites in advance.
–– On-site supervisory visits may be conducted by supervisors, GeneXpert advanced users,
national and regional TB coordinators, depending on the nature of the support to be provided.
–– All personnel conducting on-site supervision must receive training in conducting assessments
and use of checklists.
• Conducting assessments
–– On-site supervisory assessments should use standardized checklists and include discussions
with GeneXpert users, testing site management, review of Xpert MTB/RIF test site
documentation and observation of testing site operations. A supervisory checklist (Assessment
Checklist for Testing Sites or ACTS) and user’s manual are available in the Supporting
Documents/forms and templates.
–– Where possible, on-site supervisory visits should be integrated with other on-site supervision
(e.g., quarterly NTP site visits, AFB smear microscopy EQA visits).
–– Comprehensive assessments may be conducted less frequently (e.g., annually) by expert testing
site staff (e.g., GeneXpert advanced users or NTRL staff), with more frequent (e.g., quarterly)
assessments or visits done by district/regional supervisors or other appropriately trained QA
teams. The extent of evaluation during each visit will depend on the frequency of the visit,
capacity of staff and performance of the testing site (more extensive evaluation is needed in
poorly performing sites).
–– Where resources are limited, poorly performing sites should be prioritized for on-site
supervisory assessments and support. Poorly performing sites may be identified by monitoring
of performance indicators or poor performance in PT events or poor site assessment results.
27
• Providing feedback and follow-up actions
–– A plan must be established for addressing problems identified during the on-site assessment.
All problems should be discussed immediately with facility staff, and any follow-up activities
including training should be undertaken in a timely manner.
–– A list of the problems identified are included in the supervision report. Interim feedback is
given to the Laboratory Manager or facility manager immediately after the assessment. Later
the full supervision report is sent to the testing site, NTP/NTRL and designated individual for
follow-up.
–– Site supervisory reports and completed checklists should be collated and should be reviewed by
the QA or GeneXpert Focal Person.
How do I develop a site supervisory programme?
• Review the situational analysis to determine what the current coverage of site supervision is and where
the individuals conducting site supervision are located. Identify the gaps in coverage and supervisors
by mapping the testing sites to be covered
• Provide each testing site at least one supervisory visit per year by qualified supervisory staff using a
standardized checklist (link1 and link6 to situational checklist or ACTS)
• Determine the number and location of supervisors that need to be trained. Consider the additional
supervisors that are being trained as GeneXpert advanced users
• Conduct GeneXpert advanced training (http://www.stoptb.org/wg/gli/TrainingPackage_XPERT_MTB_
RIF_Ultra.asp)
• Incorporate specific aspects of site supervisory visits to GeneXpert testing sites into other training
curricula (e.g., training for regional TB coordinators)
• Develop a schedule for conducting site supervisory assessments and visits. If supervisors are limited,
focus on poorly performing testing sites as identified during review of quality indicators and PT
results and result of the testing site assessment
• Alternatively, consider piloting the programme in a few testing sites and scaling-up the programme as
the number of trained supervisors increases; or consider reducing the number of visits to all testing sites
• Review reports from site supervisory assessments to determine effectiveness & coverage of
the programme
• Report the outcomes of site supervisory visits to MOH/NTP
8.2. Proficiency testing
For many laboratory tests, the EQA program includes proficiency testing (PT). PT is a means to
determine the quality of the results generated at the testing site. PT compares testing site PT results with
a reference result (and with other laboratory results for the same panel of samples) to determine inter-
testing site comparability. The purpose of PT is to:
• Identify testing sites with serious testing deficiencies

• Help to target support to the most poorly performing testing sites
• Evaluate the proficiency of users following training
• An online up-to-date comparison of the various PT panels can be found at: (the connectivity guide is
at http://tinyurl.com/gliconnectivity)
A variety of PT panels using different sample matrices have been evaluated in a recent publication (Scott,
et al. 2014)15. Included in this evaluation were artificial sputum (WHO/GLI), dried tube specimens (CDC),
dried culture spots (National Health Laboratory Service (NHLS), South Africa) and two commercial
suppliers of lyophilized samples and liquid samples. All panels showed good compatibility with Xpert
MTB/RIF testing.
15 Scott L., Albert H., Gilpin C., Alexander H., DeGruy K. & Stevens W. 2014. Multicenter feasibility study to assess external quality assessment panels
for Xpert MTB/RIF assay in South Africa. J Clin Microbiol 52: 2493-2499
28
Alternatively, a country may elect to prepare its own PT panels (e.g., NTRL) and distribute these to
the testing sites. In-country prepared PT panels must follow a detailed SOP that has been tested and
validated and must undergo EQA. Factors affecting the decision to prepare PT panels in-country will
include capacity to manufacture panels in the country and manage the logistics of panel distribution,
data management and reporting results, cost of commercial panels, ability to manage customs clearance
and import panels from outside the country, and eligibility to participate in selected programmes.
Forms and checklists for establishing and operating a proficiency testing programme for Xpert MTB/RIF
are available in the Supporting Documents/forms and templates.
Table 6: Advantages and disadvantages of country-supplied vs externally-supplied PT panels
Country supplied Externally supplied
Advantages
Advantages • Can be initiated immediately
• Control over the frequency of testing and what is • Cost associated with testing CDC panels are minimal.
included in the PT panel However, there is a cost associated with panel and result
• Control over the scoring and analysis of data distribution
• Easily scalable • Requires minimal personnel to oversee the
programme
• No additional facilities required
Disadvantages Disadvantages
• Requires extensive planning to initiate the • No flexibility on the frequency of testing or what is
programme included in panels
• Requires external quality assessment of the PT panels • No control over scoring and analysis of data
• Cost • May not be easy to scale if the programme is over
• Requires dedicated personnel to oversee the subscribed
programme • Can be costly if multiple sites are enrolled in a paid
• Requires specialized culture facilities programme
Irrespective of the source of Xpert MTB/RIF PT panels:
• PT requirements and guidelines for testing and reporting must be communicated to the testing sites.
• When a GeneXpert instrument is installed at a new testing site, it is recommended that the site enroll
(i.e., is registered) in the PT programme.
• Testing sites should be supported to implement procedures to investigate incorrect PT results (e.g.,
performing root-cause analysis).
How do I implement a PT programme?
• Review the situational analysis to determine what PT is currently being performed

• Review the advantages & disadvantages of PT, providing options & deciding on the best approach
• If the option is to produce PT panels in-country, follow the recommendations provided in the
Supporting Documents/forms and templates
• If the option is to use an external PT panel provider:
–– Engage the provider
–– Enroll all sites in the PT programme
–– Provide the PT provider with the details of recipient of the PT reports
–– Arrange in-country distribution of PT results
–– Collate and analyse PT panel results
–– Include review of PT results as part of supervision visits
29
Element 9. Monitor performance of Xpert MTB/RIF testing
and of the QA/CQI system
Routine monitoring of quality indicators, also known as

performance indicators, is a critical element of assuring Activities at a glance
the quality of any diagnostic test (e.g., Xpert MTB/RIF)
or system (e.g., the QA/CQI system for Xpert MTB/RIF)
and is essential to inform decision-making. Performance Establish an M&E framework
indicators should include testing site performance
indicators, clinical indicators and programmatic indicators, Identify key performance and
including those that measure test results, supplies, test quality indicators
performance, PT results, and QA processes.
Collect & analyse data
9.1 Establish an M&E framework for Xpert MTB/RIF testing
and for the QA system Evaluate progress & identify
trends
The first step is to establish a framework for monitoring
and evaluation (M&E) of Xpert MTB/RIF testing and
the QA system and includes defining of performance
indicators. Table 7 lists GLI-recommended key performance indicators for Xpert MTB/RIF testing as
well as general laboratory quality indicators16 that should be monitored monthly by each testing site.
Additional indicators such as the completeness of documentation (e.g., use and completeness of registers,
logs, forms) or adherence to SOPs may be assessed during supervisory visits. For some indicators (e.g.,
proportion of specimens that are rifampicin resistant), targets are setting-specific. Laboratories should
monitor indicators and establish local targets and acceptable ranges. Deviations from expected values
should be investigated.
Whenever possible, countries should collect disaggregated data according to the population group tested
(e.g., HIV positive, MDR-TB risk, extrapulmonary TB). If the quality indicator for error rates exceeds
the target value, it should be further disaggregated to identify common error codes, in order to assist
with corrective and preventive actions. The GeneXpert platform produces electronic data and a data
connectivity solution (Element 5) should be established for remote monitoring of quality indicators.
16 GLI Practical Guide to TB Laboratory Strengthening. 2017. Available at http://stoptb.org/wg/gli/gat.asp.
30
Table 7: Key performance indicators that should be monitored monthly by testing sites
Xpert MTB/RIF Testing Quality Indicators Target
Number of tests performed, by type of test and key

Full utilization of a 4-module GeneXpert instrument is
population (e.g., HIV+, pediatric, vulnerable population,
12 tests per workday.
EPTB)
Service interruptions (stock-outs, equipment down

No interruptions
time, etc.)
Number and proportion of specimens with MTBC Dependent on population tested and country drug-
detected, rifampicin resistance not detected resistance prevalence and patterns
detected, rifampicin resistance detected resistance prevalence and patterns
Number and proportion of specimens with MTBC Dependent on population tested and country drug
detected rifampicin indeterminate resistance prevalence and patterns
Number and proportion of specimens with MTBC

Dependent on population tested and country drug
detected trace, disaggregated by patient group (For
resistance prevalence and patterns
Ultra test)
Number and proportion of specimens with MTBC not Dependent on population tested and country drug-
detected resistance prevalence and patterns
Number and proportion of specimens with errors <3%
Number and proportion of specimens with invalid

<1%
results
Number and proportion of specimens with no results <1%
Proportion of specimens tested with Xpert MTB/RIF

>95%. The target turnaround time may be modified by
for which a result was reported within 24 hrs (i.e., time
the programme based on testing schedules
from receipt of specimen to reporting of results)
In addition to these quality indicators, the testing sites should also be able to provide some of the data
needed to assess the quality of the diagnostic cascade (Table 8). Some of the indicators will also need data
from clinicians and program personnel, which may be collected routinely or using a once or twice a year
survey depending on the country capacity.
31
Table 8. Key performance indicators that should be monitored to assess the
quality of the diagnostic cascade.
Diagnostic Cascade Quality Indicators Target
Number and percentage of presumptive TB patients tested with Xpert Dependent on population tested and
MTB/RIF (End TB Strategy Laboratory Indicator 1)17 country prevalence patterns
Percentage of notified new and relapse TB cases tested with a WRD as

80% (2020)
the initial diagnostic test (Indicator 2)
Percentage of notified new and relapse TB cases with bacteriological

80% [relapse: 90%] (2020)
confirmation (Indicator 3)
Number and proportion of bacteriologically confirmed patients who

Target is setting specific
were initiated on treatment according to the national algorithm
Percentage of testing sites using a WRD at which a data connectivity

system has been established that transmits results electronically to 100% (2020)
clinicians and to an information management system (Indicator 4)
Number and proportion of Xpert MTB/RIF test results reported to

clinicians using electronic systems
Number and proportion of TB patients detected by Xpert MTB/

RIF that were reported to the TB control program, TB or MDR TB Target is setting specific
treatment focal person
Percentage of notified bacteriologically confirmed TB cases with DST

100% (2020)
results for rifampicin (Indicator 7)
Percentage of notified rifampicin-resistant TB cases with DST results

100% (2020)
for fluoroquinolones and second-line injectable agents (Indicator 8)
Number and proportion of patients with RIF-resistant TB identified

100%
by Xpert MTB/RIF testing referred for second-line DST
>95%. The ‘specified time’ should be

Proportion of specimens collected for Xpert MTB/RIF testing for
determined for each laboratory taking
which a result was received within the specified target time (i.e., time
into account testing schedules and
from collection of a specimen to receipt of results)
specimen transport schedules
>95%. The ‘specified time’ should be

Proportion of specimens referred for DST for which a result was
determined for each test required (e.g.,
received within the specified target time (i.e., time from referral of a
molecular DST or liquid culture DST) and
specimen to receipt of results)
the collection schedule used
Performance indicators for a QA system are designed to assess the performance of each of the key
features of a QA system including coverage and use of standardized procedures (i.e., SOPs), document
control, quality indicator monitoring, internal quality controls, external quality assessment, proficiency
testing, regular on-site supervision, and timely feedback, corrective actions and follow-up in all of
the facilities in the diagnostic network. Table 9 provides a suggested minimum list of indicators to be
monitored to evaluate the performance and quality of the QA/CQI system for Xpert MTB/RIF testing.
The data for these indicators should be collected monthly by the supervisory laboratories. District or
supervisory laboratories may compile and analyse the data from their jurisdictions. The data should
also be submitted to the national level for aggregation and analysis. The analyses should be done
once or twice a year. Indicators calculated using aggregate data (e.g., of testing sites labs reporting key
performance indicators (KPI)s monthly) are useful to monitor overall performance, but to facilitate
detecting problems and initiating corrective actions, it may be necessary to disaggregate the data by
region or supervisory laboratory.
17 The indicator number in parentheses refers to the number of the global indicators in the WHO Framework of indicators and targets for laboratory
strengthening under the End TB Strategy.
32
Table 9. Key indicators for the QA/CQI system that should be monitored at the
supervisory or national level
Percentage of diagnostic testing sites that are covered by a functional national system of
performance indicator monitoring and external quality assessment (EQA) (Indicator 9 of 100% (2020)
Framework18)
No. and % of testing sites enrolled in a PT programme 100%
No. and % of enrolled testing sites participating in a PT programme 100%
No and % of testing sites participating in a proficiency testing (PT) programme that

100%
successfully passed
No and % of testing sites covered by a system of supportive supervision 100%
No. and % of testing sites that have had supervisory visits in the past year 100%
No. and % of testing sites that monitor and evaluate key performance indicators at least
100%
monthly
No. and % of testing sites reporting KPIs monthly to supervisory laboratory 100%
No. and % of testing sites with standardized, competency-based job descriptions for all
100%
positions
No. and % of testing sites that have internal quality controls in place for Xpert MTB/RIF 100%
No. and % of testing sites that have a document control system in place 100%
No. and % of testing sites that have all of (and adhere to) the necessary SOPs in place 100%
Number and % of testing sites with complete quality documentation 100%
Countries should review the proposed quality indicators in line with their country guidelines and
priorities. The development of the indicators, as well as data collection and analysis, will require a
strong collaborative effort led by NTP, including laboratory services and stakeholders involved in the
programme.
A full M&E framework includes data collection tools and countries should review their existing tools to
determine which data are already being collected and which existing tools need to be revised to enable
collection of additional required data. Where necessary, additional data collection tools may be required.
The frequency of data collection should consider the feasibility and resources required for collecting
data and providing feedback, and the schedule of existing meetings at which data may be reviewed.
Adequate frequency of data collection is needed to ensure any non-conformities or lack of progress
towards targets can be acted upon in a timely manner, and that operational changes can be applied.
Programmes should establish a baseline for all performance indicators, bearing in mind that this may
only be possible for some indicators after development and implementation of new data collection tools.
Targets should be set for each indicator; this may be an absolute number or a proportion of sites meeting
a defined criterion. The national level should review progress towards meeting targets at least on annual
basis. The programme should critically evaluate reasons for not meeting targets, put in place corrective
actions and set targets for the next year.
18 This is indicator 9 of the WHO Framework of indicators and targets for laboratory strengthening under the End TB Strategy. 2016. World Health
Organization. Available at http://www.who.int/tb/publications/labindicators/en/
33
9.2 Assign responsibilities for data collection, reporting and analysis
All testing sites should collect and analyse testing data on at least a monthly basis, using a standardised
format. Targets should be set for all indicators monitored (usually by the national programme following
consideration of GLI guidance), and any unexplained change in quality indicators, such as increase in
error rates, a change in MTBC positivity rate or RIF-resistance rate, or a significant change in volume
of tests conducted, should be documented and investigated. A standard set of quality indicators should
be used for all sites conducting a particular test to allow for comparison. Quality indicators should be
reviewed by the laboratory manager and quality officer and must always be linked to corrective actions
if any unexpected results or trends are observed. Documentation of corrective actions and subsequent
improvement and normalization of laboratory indicators following the corrective actions are critical.
A system should be in place for centralized reporting of monthly quality indicators to the supervisory
laboratory, regional QA officer (if applicable), NTRL or NTP. The appropriate QA officers or manager
or data units should review and analyze the reported data. For Xpert MTB/RIF testing, the use of
diagnostics connectivity solutions (Element 5) will allow for real-time remote monitoring of sites within
a network and provide the capacity to easily and accurately stratify data as needed for analysis
of performance.
After reviewing existing tools and making necessary revisions to capture the information required for
performance indicators, countries should allocate responsibility for data collection, compilation (e.g., by
region and nationally) and analysis of results. This can be recorded in the M&E framework document.
Data for most indicators will be collected by laboratory staff at each testing site, with support from
advanced users or supervisory staff. These data will need to be compiled into a regional and/or national
level data set for all sites.
Responsibilities for data collection, a system for sending data to regional and/or national level, and
responsibility for data analysis and reporting should be clearly defined. Individuals responsible, and
not just institutions, should be named and provided with appropriate training and tools to undertake
the applicable activities. Mechanisms for feedback of data and reports, including recommendations for
action items, should be established and clearly communicated to all involved.
Where possible, use existing cadres, e.g., advanced users, and incorporate data collection for M&E into
existing supervision and technical support activities.
The M&E programme is the overall responsibility of the NTP, led by the programme manager, with
other programmes and institutions critically involved, including National AIDS Control programme,
Department of Laboratory Services, MOH, and health facilities. All M&E reports should be prepared
and provided to the NTP manager for review, finalization and approval, prior to being disseminated
to stakeholders.
34
9.3 Collect, compile and analyse data
Based on the M&E framework, data collection tools should be developed for data collection at different
levels, from testing site data, district and regional patient-related data (e.g., treatment initiation) to
national level data (e.g., training and PT programme). Examples of data collection and analysis forms for
key performance indicators are available as Microsoft Word documents in the Supporting Documents/
forms and templates. The data collection and analysis forms are also available in an Excel format that
can automatically calculate the indicators when the required data are entered.
How do I collect, compile and analyse data?
• Identify who will collect the data (e.g., users, regional TB coordinators, National QA Unit, GeneXpert
advanced users)
• Assign responsibility for developing data collection tools, for example, to the National QA officer or
M&E manager
• Develop data collection tools and incorporate these into existing tools where possible (e.g., supervisory
visit checklists)
• Schedule training for data collectors at all levels (site level, regional level, super users, national level,
programme)
• Establish and communicate deadlines for reporting of data, based on data collection frequency, timing
of review meetings and monitor adherence of data collectors to the schedule
• Compile a performance indicator report on quarterly, biannual and annual basis
• Prioritize the introduction of remote monitoring to assist with collection of instrument data on test
performance
Basic analysis of performance indicators compared with the targets should be conducted locally (e.g., at
each testing site) and these data used for local decision-making. That is, where possible the testing site
staff should analyse their data to detect problems (e.g., high error rates), conduct a root cause analysis
and initiate corrective actions. Such a local review and follow up should not wait for regional or national
analysis to take place. In some cases (e.g., unexpected high rates of RIF resistance), assistance from the
supervisory site will be needed to analyse the problems and develop and initiate corrective actions.
Remote connectivity systems enable basic automated analyses and alerts which will facilitate this local
analysis and use of data for action. Data may be exported for more in-depth or specialized analysis such
as the analysis of individual indicators and groups of indicators (e.g., those relating to quality) at the
regional or national level.
35
9.4 Evaluate progress and identify trends
QA and quality improvement are a continuous and cyclical process. QA activities should be phased in
until all testing sites have been covered in all areas. This will require continual sharing of best practices,
lessons learned and planning. Furthermore, expansion of testing services to additional sites, either by
strengthening of referral networks or by installing new instruments, should be planned in a rational
manner, with due attention paid to new services meeting required quality standards from the outset.
Data should be collected and initially reviewed at the local testing site level. Trends that require
intervention (e.g., increase in proportion of unsuccessful results [errors, no results, invalid results, and
interrupted runs], increase in service interruption) must be communicated, appropriate corrective
actions must be undertaken and impact of the interventions reviewed. Furthermore, analysis of regional
or national level data will identify trends that extend beyond individual sites (e.g., reagent batch issues,
PT, or equipment maintenance).
Measuring of impact performance indicators will highlight areas for improvement around translating
rapid diagnostic results into rapid initiation of appropriate care and treatment, and ultimately improved
patient outcomes.
The NTP needs to work with stakeholders to develop annual goals so that they are understood and
embraced by everyone contributing to Xpert MTB/RIF QA, and so that partner activities are aligned
with NTP priority needs and the overall implementation framework. At least one annual review of all
performance indicator data should be conducted at the national level, under the leadership of NTP, with
laboratory and clinical experts and with the participation of all relevant stakeholders.
How do I evaluate progress towards targets?
• Review the performance indicators compared with annual and 5-year targets
• Prioritize, plan and budget for future activities
• Review and revise implementation strategies, if needed, to meet the goals
• Engage stakeholders in the review and re-programming
36
Element 10. Strengthen the clinical-laboratory interface and the
diagnostic cascade
A comprehensive system to ensure the quality of

laboratory testing must address all the relevant parts Activities at a glance
of the diagnostic cascade, not just what happens in
the laboratory. Published literature on a variety of
laboratory tests highlights that factors that have the Provide training on the
largest impact on quality of diagnostic services occur diagnostic cascade to all
in the pre-pre-analytical phase (choice of test, etc.) and laboratorians and healthcare
post-post-analytical (interpretation of results and patient workers
management). Indeed, data from South Africa19 suggests
that even in a well-managed laboratory network, gaps still Develop SOPs for the clinical-
exist in ensuring rapid referral of all diagnosed patients laboratory interface
to treatment.
Develop systems to support the
At the national and supervisory level, efforts should flow of information between
concentrate on training, developing SOPS and systems. clinicians, program staff, and
Guidance on technical aspects of collecting quality laboratorians
specimens and reporting accurate results are described in
Element 10 of Part 2 below. Monitor the performance of the
diagnostic cascade
How do I strengthen the clinical-laboratory interface?
• Provide training to laboratorians, nurses, clinicians and other healthcare workers on the aspects of the
diagnostic cascade that affect the quality of TB testing
• Ensure that national testing algorithms are followed and that the correct test is ordered for each
presumptive TB patient
• Develop SOPs for collecting quality samples and promptly submitting them to the testing site along
with a properly completed test requisition form
• Develop SOPs and forms to ensure that accurate results are reported to clinicians, TB control officers,
and TB and MDR TB treatment focal persons and include information on the interpretation of the
test results
• Develop systems to support the flow of information between clinicians, program staff and
laboratorians and establish procedures for regular meetings of staff to discuss issues, troubleshoot
problems and strengthen the clinical-laboratory interface
• Monitor the performance of the diagnostic cascade (see Element 9)
19 Naidoo et al. 2017. The South African Tuberculosis Care Cascade: Estimated Losses and Methodological Challenges. J Infect Dis 216 (suppl_7):
S702–S713, https://doi.org/10.1093/infdis/jix335
37
Part 2: QA for Xpert
MTB/RIF Testing Sites
Background
This section of the guide focuses on the QA activities at the testing site that are essential to the provision
and documentation of quality testing. For laboratories that are pursuing accreditation to IS15189
standards, the QA activities described here are closely related to the twelve Quality System Essentials
(QSEs) that direct and control an organization with regard to quality from the basis of a quality
management system (QMS). The reader is referred to the WHO Laboratory Quality Management
System: Handbook (2011)20 for an in-depth discussion of QMS and QSEs. Table 10 shows the relationship
of the QA activities described in this section with the QSEs.
Standards and key activities for assuring quality
Quality standards are goals toward which efforts and resources to assure quality Xpert MTB/RIF testing
should be directed. Standards that were developed to measure the performance of the TB diagnostic
network form the basis of the standards for the Xpert MTB/RIF QA system. The TB diagnostic network
standards are based on standards developed by the Global Laboratory Initiative (GLI) for ensuring
the quality of AFB smear microscopy21, by the African Society of Laboratory Medicine (ASLM) and
Association of Public Health Laboratories (APHL) for evaluating diagnostic networks22, and by USAID
and partners for evaluating TB diagnostic networks in Nigeria and India23. The standards, associated key
QA activities, and corresponding sections of this guide are described in Table 10.
The national and supervisory levels are responsible for the processes and systems needed to ensure
quality testing in all facilities and includes developing national policies and procedures; monitoring
and evaluating performance indicators; conducting external quality assessment and proficiency testing
programs; and providing supportive supervision. At the individual testing site, the QA system focuses
on the processes and procedures to ensure the quality and reliability of each test performed in the
laboratory and a well-functioning laboratory-clinical interface to ensure efficient referral for testing,
prompt reporting and linkage to care of diagnosed patients.
20 WHO Laboratory Quality Management System: handbook. 2011. (http://www.who.int/ihr/publications/lqms/en/)

21 TB Microscopy Network Accreditation. An assessment tool. Global Laboratory Initiative. 2013. http://www.stoptb.org/wg/gli/assets/documents/
TBMicroscopy_Network_Accreditation_Web.pdf
22 Ondoa, P. et al. A new matrix for scoring the functionality of national laboratory networks in Africa: introducing the LABNET scorecard. African
Journal of Laboratory Medicine, 5, Oct. 2016. http://www.ajlmonline.org/index.php/ajlm/article/view/498/712
23 Albert, H. Essential standards for a TB diagnostic network. ASLM 2016.
38
Table 10: Diagnostic Network Standards and Key Quality Assurance Activities
GLI Standard Key QA Activities
Structures and policies are in place Governance (Element 1)24

that enable continuous, country-wide • Appoint, train, and empower quality officers
availability of free, quality assured Planning (Element 2)
diagnosis according to the national • Participate in a situational analysis and development of a
guidelines. prioritized action plan.
A minimum package of tests and quality Quality assurance documentation (Element 3)

standards is defined for each level of the • Use standardized documents and forms for sample request and
TB diagnostic network. results recording and reporting at all testing sites
Adequate numbers of competent, well- Training and certification (Element 4)

trained and motivated technical and • Train at least two users from each site and assess competency
managerial staff are available at all levels • Train sufficient advanced users to provide supervision and
of the diagnostic network. advanced troubleshooting
Inter-operable and inter-connected

electronic recording and reporting Data connectivity and remote monitoring (Element 5)
systems are in place that generate reliable • Utilize remote monitoring systems to collect and analyse data
data that are monitored and analysed in relating to performance indicators, QA and procurement
real time.
Testing is performed in a manner and in A safe and functional testing site (Element 6)
facilities that ensure safety for the staff, • Ensure that the site is not hazardous for the staff, patient or
the customers, the community and the environment
environment. • Ensure that a good working environment is available
Supply chain (Element 7)

• Ensure uninterrupted supply of Xpert MTB/RIF supplies and
reagents
Testing is performed with state-of-the-art
• Perform new lot testing on new batches of reagents
and well-maintained equipment and an
Equipment servicing and maintenance (Element 7)
uninterrupted supply of quality reagents
• Ensure that all GeneXpert instruments undergo routine
and consumables.
maintenance and calibration
• Verify all instruments as fit for use at installation, after service or
calibration, or after moving instruments
Proficiency Testing (PT) (Element 8)

• Enroll in a PT programme
Continuous quality improvement targets
• Investigate incorrect PT results and take corrective actions
all facilities within the network and
Site supervision (Element 8)
includes quality indicator monitoring,
• Receive on-site supervisory visits on a regular basis (at least yearly)
external quality assurance, and regular on-
by competent personnel
site supervision.
Monitoring and evaluation (Element 9)
• Collect, analyse and report performance indicator data monthly
Strengthen the clinical-laboratory interface and the diagnostic

cascade (Element 10)
• Ensure that national testing algorithms are followed and that the
An efficient diagnostic-clinical interface correct test is ordered for each patient
allows for appropriate diagnostic tests to • Ensure that quality specimens are collected, properly labelled,
be ordered and performed and ensures correctly stored, and promptly transported to the testing site
the timely linkage of diagnosed patients to • Enforce the use of standardized test requisition forms
appropriate care and treatment • Report accurate results to clinicians and TB and MDR TB treatment
focal persons and include information on the interpretation of the
test result
• Monitor the performance of the diagnostic cascade
24 The element numbers correspond to the numbers of the sections of this guide that describe the activities needed to accomplish the standard.
39
Pillars of a Quality Assurance System
National Planning Procedures & training Testing infrastructure Monitor impact

& supplies
• Governance • Quality procedures • Remote monitoring
• Situational analysis & documentation • Safe & functional site • External quality
• Planning & budgeting • Training & certification • Equipment & supplies assessment (EQA)
• Clinical–laboratory • Data connectivity • M&E
interface
At the Xpert MTB/RIF testing sites, the key steps in quality assurance include:
1. Governance: Appoint, train and empower a quality officer. The quality officer should report to the
head of the laboratory and must have the authority to implement and enforce the quality assurance
programme. Quality assurance or quality improvement officers should also be appointed at
participating clinical sites to oversee the quality of the clinical and diagnostic services.
2. Planning: Develop a costed prioritized action plan for phased implementation of the required QA
activities that aligns with national and regional plans. Adequately budget the activities and set a time
line for implementation and monitor progress.
3. Quality procedures and documentation: Enforce adherence to SOPs, use standardized requisition,
recording and reporting forms, and maintain documents and records.
4. Ensure GeneXpert users are trained: Train all GeneXpert users in the operation of the GeneXpert
instrument, performance of the Xpert MTB/RIF test, and quality assurance activities and assess and
document their competency.
5. Diagnostics connectivity and remote monitoring: Establish and maintain a remote monitoring
system to collect and analyse data relating to performance indicators, QA and procurement.
6. Make the testing site safe and functional: Ensure the environment is clean, secure, temperature-
controlled and has adequate uninterrupted power.
7. Equipment and supplies:
a. Maintenance and calibration of the GeneXpert instrument: Verify that the GeneXpert
instrument is functioning properly.
b. Regularly maintain and calibrate the instrument according to the manufacturer’s
recommendations.
c. Ensure adequate supplies & reagents: Implement a process to ensure an adequate,
uninterrupted supply of quality-assured reagents.
8. Participate in an EQA programme: The EQA program should include proficiency testing, on-site
evaluations, and supportive supervision; analyse EQA results; take corrective action if needed and
document follow-up.
9. Monitor performance of Xpert MTB/RIF testing and the QA system: Regularly monitor, analyse,
and report performance indicators.
10. Clinical-Laboratory interface: strengthen the clinical-laboratory interface to ensure that national
testing algorithms are followed, the correct test is ordered for each patient, quality samples are
collected and submitted to the laboratory, accurate results are reported to the clinician, results are
correctly interpreted and patients are promptly placed on appropriate therapy.
40
Detailed guidance is provided in the subsequent sections for each of the individual elements. Note:
The elements are described in a logical order to ensure implementation of a functioning QA system,
but the order is not meant to be a prescriptive step-by-step order (i.e., complete element 1 before
element 2, etc.). As part of the strategic planning process (see Part 1, Element 2), countries will prioritize
the activities and develop a phased implementation plan and time line. Such plans should focus on
providing the appropriate structures (e.g., quality teams, data monitoring units), support (e.g., training,
supportive supervision, constructive feedback) and monitoring and evaluation processes (e.g., collection
and regular analysis of key performance data) needed to implement a functioning continuous quality
improvement process. For example, implementing a proficiency testing program without implementing
a corresponding system of timely feedback, corrective actions and supervisory visits will greatly limit the
usefulness and impact of the proficiency testing program on the quality of testing.
The following sections in this guide describe practical steps for the implementation of a system for
ensuring the quality of Xpert MTB/RIF testing at the testing site level. (Part 1 provided guidance for
the national and supervisory levels). This part is divided into sections, each dealing with one of the
QA elements (Table 10) required for assuring a quality Xpert MTB/RIF test result. Links to additional
resources are provided at the end of the guide. Hyperlinks to tools and job aids to assist with the
implementation of QA activities are provided. These templates can be customized as required.
41
Element 1. Governance
The governance structure of Xpert MTB/RIF QA activities

at the testing site is an extension of the governance Activities at a glance
structure at the national level (see Part 1, Section 1) and
requires clearly defined roles and responsibilities.
Establish a governance structure
At smaller facilities, the laboratory manager will be
responsible for overseeing QA activities. At larger facilities, Appoint, train, and empower a
there may be a Health Facility Quality Committee QA officer
(HFQC) which provides oversight and coordination for
QA activities at the facility and provides regular progress
reports to the supervisory levels. If so, the Xpert MTB/
RIF testing site may be able to rely on the HFQC for oversight of Xpert MTB/RIF QA. In this case, it
will be essential that the Xpert MTB/RIF testing site is represented on the HFQC to ensure adequate
communication and translation of policy into action. In addition, the person responsible for the Xpert
MTB/RIF testing should be trained in basic QA procedures and report to the HFQC.
Table 11. Example of a testing site governance structure with defined roles and responsibilities
Position Roles and responsibilities
• Ensure accountability, leadership and governance at health facility level

Health Facility
• Provide oversight and coordination for QA and CQI activities at the institution
Quality Committee
• Provide regular progress reports to the regional QA structure
(if applicable)
• Translate policy into practice
• Oversee and enforce TB QA policies and procedures at the testing site

• Appoint a QA officer
Laboratory manager
• Supervise collection of data and analysis of quality and performance indicators
• Troubleshoot problems and initiate corrective actions
• Oversee and direct the execution of the Xpert MTB/RIF QA processes and procedures at
the testing site
Quality assurance
• Oversee implementation of corrective actions
officer
• Participate in the collection of data and analysis of quality and performance indicators
• Report directly to the testing site and laboratory manager
• Adhere to all QA policies and procedures

Xpert user
• Assist with the collection of data, troubleshooting, and corrective actions
What you need to do
Steps in establishing a governance structure at the testing site include:
• Develop an organogram of the governance structure that clearly defines relationships and lines of
supervision
• Assign roles and responsibilities and develop terms of reference
• Establish lines of communication and reporting within the governance structure of the testing site and
the national and regional QA networks.
• Map out the flow of information and identify points of contact.
A key step is for each Xpert MTB/RIF testing site to appoint a quality officer (full-time or part-time) or
assign the duties of a quality officer to an existing staff member. The quality officer would be responsible
for overseeing and directing the Xpert MTB/RIF QA processes at the testing site and reporting directly to
the testing site and laboratory manager. In many laboratories, the QA officer might be responsible for QA
of all testing done at the site.
Quality assurance or quality improvement officers should also be appointed at participating clinical sites
and empowered to oversee the quality of the clinical and diagnostic services.
42
Element 2. Planning
The planning process should include 1) a situational

analysis to determine the current status of testing and Activities at a glance
quality practices and the implementation of Xpert MTB/
RIF QA activities at the testing site, 2) development of a
costed prioritized action plan for phased implementation Participate in a situational
of the required QA activities with targets and a time line analysis
and 3) allocation of an adequate budget for QA activities.
Assist with the development of
What you need to do an action plan
2.1. Situational analysis Assist with the development of

a QA budget
A situational analysis is needed to determine which Xpert
MTB/RIF QA activities are currently implemented at the
testing site and their impact on quality of diagnosis and to identify the gaps in providing quality assured
Xpert MTB/RIF results. The situational analysis will most likely be done by the National QA Officer or
the supervisory laboratory QA Officer using the Situational Analysis Checklist and ACTS . The situational
analysis report will describe gaps identified, recommendations for how to implement quality assurance
activities and propose a time line for implementation. An excerpt from an example situational analysis
checklist, with commonly observed outcomes and recommendations is provided.
The testing site staff should review the Situational Analysis Checklist and collect all of the documents
(e.g., policies, procedures, SOPs, test requisition forms, result reporting forms, logbooks, registers, etc.)
needed for the assessment.
The testing site manager or laboratory manager should review the situational analysis report and work
with the supervisory laboratory personnel to develop an action plan including time lines to address the
recommendations.
2.2. Budget
• Working with the state, region and facility officials, the testing site should assist with the development
of a budget that addresses both the implementation of recommendations from the situational analysis
and the implementation and continuance of the QA activities thereafter. A GeneXpert costing tool
is available on the FIND website: https://www.finddx.org/implementation-resources/#tb planning and
resources (both financial and human).
Table 12: Budgetary considerations for QA activities
QA activity Budgetary considerations
• Preparing and printing of standardized sample request and results reporting

Generate QA documentation forms, SOPs, etc.
• Preparing and printing of standardized logbooks
Maintain and service equipment • Site upgrades, calibration kits and warranty costs
Training & certification • Costs associated with training including travel, accommodation, materials, etc.
Onsite supervisory visits • Costs associated with hosting an on-site visit and preparing documents
• Costs associated with testing PT panels

PT testing
• Costs associated with procuring PT panels, if done at site level
• Material cost per test, including but not limited to Xpert MTB/RIF test
Strengthen the supply chain
reagents, consumables, sample collection items, printing paper, etc.
Remote monitoring • Costs associated with installing and maintaining a remote monitoring system
43
Element 3. Quality procedures and documentation
Without accurate and complete documentation, the quality

of Xpert MTB/RIF test results may be compromised. Activities at a glance
Standardized documents, forms and SOPs (developed at
the national level) should be available and adhered to at the
testing sites and participating clinical sites. The documents Receive documents from
must address activities throughout the diagnostic cascade supervisory or national level
including documentation for clinical activities (e.g.,
specimen collection and referral) and laboratory activities. Customize documents by
Documents and records must be up-to-date, accurate adding testing site-specific
and readily accessible. A document control system is information
needed to ensure regular review of quality management
documents (e.g., SOPs) and to ensure the correctness of the Implement a document control
documentation that support laboratory testing, which in system
turn increases quality assurance.
Ensure users read & understand
What you need to do the QA documents
Each testing site will need to receive and tailor the required
QA-related documents by adding site specific information,
creating and implementing a document control system, and ensuring that all users read and understand
the documents. The priority for each site should be to implement standard SOPs, including training of
staff on the use of the SOP.
Activity How do I achieve this?
• Obtain the required documents (should be available from NTRL, see Part 1)
• Review the documents, customize as needed for the testing site (e.g., insert site
specific contacts), but do not alter the test procedure
• Sign and date the document to indicate review and approval
Generate QA-related • Print and disseminate the approved documents
documentation • Post job aids at the testing bench
• Provide training in the use of the documentation
• Ensure all staff have read documents and signed as proof of reading
• Make sure obsolete versions of SOPs are removed and the most recent version is
accessible to all staff
• Have each user review all documents annually

Ensure users read and
• Provide training on the documents
understand the QA
• Have each user indicate that they have read and understood by signing in the place
documents
provided on the form
• Obtain the SOP for Document Control

• Create a Document Retention List: determine the storage time and location for all
documents used
• Make a document control log and document revision form
Create a document control • Add a front page to each quality document used in the laboratory to track versions
system • Create folders for storing SOPs at a convenient location for staff to have access to
the SOPs when needed
• Develop personnel files for all staff members to document their knowledge of the
correct documents
• Roll out the document control system
44
Table 13: SOPs, forms, and documents that must be available at the testing sites
Resource Description
Describes a step-by-step protocol for diagnosis of TB at

National TB Diagnostic Algorithm
healthcare facilities
Describes the procedures to be followed to ensure

Specimen collection and transport SOP
collection of good quality specimens and safe, rapid
transport of specimens
Document Control SOP Describes the procedures to ensure that the correct
http://www.gliquality.org/activities/2/33 documentation (e.g., SOP) is used for laboratory testing
Xpert MTB/RIF test SOP Describes the procedures for performing the Xpert
https://www.finddx.org/implementation-resources/#tb MTB/RIF test
Xpert MTB/RIF Ultra SOP Describes the procedures for performing the Xpert
https://www.finddx.org/implementation-resources/#tb MTB/RIF Ultra test
Test requisition form Form for requesting Xpert MTB/RIF testing
Register for recording patient, specimen, and test

Laboratory test registers
information
GeneXpert maintenance Log Form for recording GeneXpert maintenance tasks
Temperature monitoring Log Form for recording daily temperature monitoring in

https://www.finddx.org/implementation-resources/#tb testing and kit storage areas
Non-conformity and corrective action log Form for capturing non-conformities and corrective
http://www.finddx.org/tb/ actions
Describes the procedure of safely disposing

Waste management SOP
consumables and Xpert MTB/RIF reagents (may be
included in a Biosafety SOP)
Describes the procedure to follow in the event of a

Spill management SOP
biohazard spill at a testing site (may be included in a
Biosafety SOP)
Xpert MTB/RIF WHO reporting codes Describes the standard WHO reporting codes for
http://www.who.int/tb/publications/definitions/en/ reporting Xpert MTB/RIF test results
Form for capturing Xpert MTB/RIF performance

Xpert MTB/RIF performance indicator reporting form
indicator data
Xpert MTB/RIF test reporting form Form for reporting Xpert MTB/RIF test results to
http://www.who.int/tb/publications/definitions/en/ clinicians
Describes the general procedure for testing PT

Proficiency Testing (PT) SOP samples, resulting, reporting, and corrective action for
unacceptable results
Form for documenting the results of the investigation

PT failure investigation and corrective action form
of PT failures and remedial action taken
45
Element 4. Training, competency assessment and certification
GeneXpert users must be trained in the operation of the

GeneXpert instrument, correct performance of the Xpert Activities at a glance
MTB/RIF test and carrying out the associated QA activities.
Advanced users receive additional training that assists in
the implementation of the Xpert MTB/RIF test. Clinicians Train users in the operation of
and other clinical staff must be trained on the diagnostic the GeneXpert instrument, Xpert
algorithm, ordering tests, collecting specimens, submitting MTB/RIF test and QA activities
samples and interpreting results. The competency of all
users must be regularly assessed. Failure to adequately Assess users for competency
train and assess users can impact quality:
• Poorly trained staff may perform the Xpert MTB/RIF

test incorrectly and report out inaccurate results
• Poorly trained staff are less productive than well-trained competent staff
• Failure to adhere to SOPs leads to inconsistent requesting, testing and reporting of Xpert MTB/RIF
test results leading to possible errors and confusion for clinicians
• Poor quality results cause clients, patients and clinicians to be dissatisfied and could lead to a lack of
confidence in the quality of the service
• Lack of trained advanced users may delay troubleshooting and corrective actions at the testing sites
What you need to do
4.1. Provide training for Xpert MTB/RIF users, advanced users, and clinicians
Training and certification activities and procedures must be clearly developed, documented and
executed in line with international standards. A standardized Xpert MTB/RIF training programme
should be available from the NTP or NTRL and include training curricula for trainers, users, advanced
users and clinicians. Standardized training material is available from the Global Laboratory Initiative25
including training packages on the Xpert MTB/RIF test and on programmatic aspects of diagnostic
laboratory strengthening.
• Using a standardized curriculum, users must be trained in operating the GeneXpert instrument and
performing of the Xpert MTB/RIF test and the associated QA activities. Users must pass a competency
assessment before beginning testing.
• Advanced users must be trained to co-ordinate Xpert MTB/RIF test QA activities such as supervisory
visits, competency assessments and troubleshooting. Advanced users are selected from the group of
certified users by trainers based on their aptitude and temperament to perform advanced GeneXpert
functions. Advanced users are certified as competent following a competency assessment.
• Clinical trainings should be conducted as part of the continuous medical education of healthcare and
clinical staff to ensure an understanding of the uses for the test and its limitations, and to provide
updated information. Testing site managers may be required to sensitize staff from referring sites on
the Xpert MTB/RIF assay and provide training on ordering of tests, completing request forms and
interpreting test results.
25 http://www.stoptb.org/wg/gli/trainingpackages.asp
46
User (and advanced user) trainings are often coordinated and conducted centrally (e.g., by NTRL),
regionallyor at site level. The activities of the testing site managers typically include:
• selecting staff for training

• assessing (or delegating the assessment to users that have achieved a competency level of 4 or 5) and 3)
documenting the competency of each user (see below)
• scheduling refresher training with competency assessment below level 3
• preparing staff duty roster to ensure regular rotation of trained users on the Xpert MTB/RIF
testing bench
4.2. Conduct and document competency assessments
Competency in a procedure must be measured and documented26. Competency assessments are based
on the staff’s actual skills and knowledge. Competency assessments for users are performed both at
the end of the training and at the testing site according to the testing site’s training plan (e.g., twice a
year)27. Advanced users should be assessed at the end of the GeneXpert advanced user training and
regularly (usually annually or bi-annually) thereafter. Competent users are issued with a certificate and
competency documented in their personnel file.
26 The competency assessor must be competent in the procedure to identify deviations from the SOP.
27 Competency assessments may be performed more frequently under special circumstances (e.g., following refresher training courses).
Testing sites may wish to include competency assessments at the beginning of an Xpert MTB/RIF test user rotation, if the time between rotations
exceeds three months.
47
Level Competencies required How do I achieve this?
• Operating and understanding basic

maintenance of the GeneXpert instrument • Users must be trained using the
Users
• Performing the Xpert MTB/RIF test standardized curriculum
• Recording & reporting results using – Through training, users must acquire the
standard registers & tools necessary skills to be certified competent in
• Carrying out and documenting all required the Xpert MTB/RIF test procedure
QA activities.
• Advanced users must be trained using the

• In addition to the recommendations for
standardized curriculum
users, advanced users must be competent in
Advanced users – Through training, advanced users
supervisory visits, competency assessments,
must acquire the necessary skills for
troubleshooting & and advanced
troubleshooting, supervision & performing
maintenance procedures
competency assessments
• Providing supervision & coaching to

users, analysing quality assurance data, • Testing site managers should have a basic
troubleshooting & implementing corrective understanding of the GeneXpert instrument
Testing site
action and Xpert MTB/RIF test
managers
• Managing site cartridge supplies – Testing site managers must receive training
• Communicating with supervisory in QA data analysis & procurement
laboratory, suppliers, and service providers
• Adhering to national testing algorithm

• Ordering of the appropriate test for a
patient
• Clinicians must receive training in
Clinicians • Completely filling in the correct test
application of the national testing algorithm
requisition form
• Collecting & submitting specimens for
testing
• Identifying patients that are eligible for

Xpert MTB/RIF testing
• Health screeners must receive training in
Health screeners • Referring patients for Xpert MTB/RIF
the national testing algorithm & identifying
testing
patients eligible for Xpert MTB/RIF testing
• Collecting and submitting specimens for
testing
48
Element 5. Diagnostics connectivity and remote monitoring
Diagnostics connectivity refers to the ability to connect

diagnostic test devices that produce results in a digital Activities at a glance
format, such as GeneXpert instruments. Connected devices
can transmit data automatically to 1) clinicians and patients
which allows for faster patient follow-up, 2) laboratory Work with national level to
information management systems or electronic registers, determine which diagnostic
reducing staff time and the chance of transcription errors connectivity system will be used
and 3) the NTP to assist with surveillance of trends on
disease or resistance patterns. Obtain & install all needed
hardware & equipment
In addition, these systems offer the ability to manage
inventory, conduct QA and remotely monitoring Identify and train users
performance:
Implement SOPs
• Software can track consumption and inventory to avoid
stock outs and expiring cartridges as well as potentially Establish lines of communication
identify cartridge lots or instruments (modules) with
poor performance and abnormal error rates.
• Software can rapidly and automatically calculate many
of the key performance indicators and greatly facilitate the monitoring and evaluating processes.
• With remote monitoring, designated persons can get an overview of the facilities, devices and
commodities in their network. For, example, the head of a supervisory laboratory can easily see how
many tests are being performed and where and which sites are underperforming or experiencing
abnormal results or errors, which may highlight a need for corrective action.
Because of the promise to improve recording, reporting and monitoring of data and performance
indicators, diagnostics connectivity solutions, especially for Xpert MTB/RIF testing, are the way of the
future and countries should give high priority to investing in developing and maintain such systems and
in training personnel to operate the systems and to use the data generated for decision making.
Diagnostics connectivity solutions typically comprise: 1) a connectable diagnostic device that produces
electronic data, 2) a software platform that receives and interprets data and 3) a means to transmit data
from the device to the software platform and to a server. Systems have been developed by Cepheid, USA
(C360), SystemOne (GxAlert™/Aspect™), Savics (DataToCare™) and Blue Frontier (Connected Diagnostics
Platform). The systems connect GeneXpert instruments to central in-country servers or cloud-based
servers via the internet or SMS. Instrument data can be accessed via web-based dashboards. The software
can usually be configured so that subsets of data can be securely made available to those that need access
to them. Security protocols also protect the privacy of the patient.
49
The decision to implement a diagnostics connectivity solution will likely be made at the national level.
The testing site staff will need to work with the national and supervisory levels to operationalize the
system at the testing site. Important considerations at the site level are:
• What hardware and software will need to be installed and maintained at the testing site?
• Will internet or cellular service be used and what is the quality and reliability of the service?
• Who will have access to the data at the site?
• What training will be required for testing site staff to access the system?
• How will data be secured?
• How, and at what frequency, is the system backed-up?
• What is the availability of information technology support on-site or remotely and what are the
computer skills of the users?
• What are the associated costs of implementing and maintaining a remote monitoring system (e.g.,
internet access charges, information technology support, software licenses)?
Details of diagnostics connectivity solutions may be found in the GLI Quick Guide to TB Diagnostics
Connectivity Solutions28.
How do I establish a data connectivity solution?
• Work with national level to

–– determine which diagnostic connectivity system and communication system will be used
–– obtain and install all needed hardware and equipment, e.g., routers, modems, server,
or SIM cards
–– set up the connectivity solution
• Determine which staff members will have access to the system and to which data or features
• Have all users participate in implementation workshops and trainings that include data collection,
data use and management, and day-to-day operations of connectivity solution
• Implement SOPs for access, reporting, data entry, data security and data back-up
• Arrange for on-site or remote information technology support
• Establish lines of communication with the national, regional or local units that will remotely
monitor data
28 GLI Quick Guide to TB Diagnostics Connectivity Solutions. GLI. 2016. http://stoptb.org/wg/gli/gat.asp.
50
Element 6. A safe and functional testing site
In a functional testing site, the GeneXpert instrument will

be properly positioned on a vibration-free workbench in Activities at a glance
a clean, secure location and there will be an uninterrupted
supply of power and appropriate working and storage
temperatures. In a safe environment, WHO biosafety Place the GeneXpert correctly
recommendations for conducting the Xpert MTB/RIF
test will be followed with adequate ventilation (although Secure the GeneXpert
the instrument should not be placed directly under an instrument from theft
air-conditioning unit), appropriate personal protective
equipment (PPE) will be used and biological waste will Ensure an uninterrupted power
be disposed of safely and in accordance with regulations. supply
Failure to provide a safe and functional work environment
can impact the quality of testing in several ways including: Ensure an optimal working
temperature
• An unsafe testing site is a hazard to staff, patients, the
community and the environment Perform a risk assessment
• In a poorly maintained or dirty testing site, specimens
may become contaminated or cross-contaminated Ensure sufficient ventilation for
leading to inaccurate or incorrect results testing procedures
• In an unsecure testing site, test results may be delayed if
there is equipment failure or theft Provide suitable PPE and train
• Testing sites that do not maintain uninterrupted power, staff in its correct use
optimal working temperature, and a clean environment
can have equipment failures and high error rates that Discard waste as recommended
delay reporting and waste cartridges
Use appropriate disinfectant and
What you need to do prepare correctly
6.1. Create and maintain a functional working environment
The working environment should consider placement and security of the GeneXpert instrument, power
supply and operating conditions.
51
Considerations & Activities How do I achieve this?
• Place the instrument in a sheltered environment, preferably on a stable

The GeneXpert is a precision bench with at least 5 cm of clearance on either side.
instrument designed for operation • Do not place the instrument close to the vents of other instruments or air-
indoors. handling units.
The GeneXpert must be protected • Remove clutter and enable clear access to the computer and module units.
from dust. • Do not place the instrument in a thoroughfare where it may easily be
bumped.
• Access to testing areas should be restricted to authorized staff.

Unaccompanied visitors should not be allowed in testing areas.
Security measures and access
• Provide security measures of security locks, security bars and doors, if
control to the testing site are
possible.
required to prevent theft of the
• Do not allow security measures to impair general safety nor be in violation
GeneXpert instrument or the
of local regulations for escape routes in the case of fire or other emergencies.
computer.
• Secure instruments and the computer by a Kensington security lock or
similar theft deterrents.
Uninterrupted power is needed • Use an uninterrupted power supply (UPS) to support the instrument in the
to support the instrument in the event of a power interruption for at least the test duration (2 hours).
event of a power interruption. • Refer to the guidance document to determine appropriate selection of UPS.
The optimal operating

temperature for the GeneXpert
instrument is 15-30°C. The relative • Depending on the local setting sites may require air conditioning units to
humidity must be between 10%- be installed in the testing site and/or storage area.
95% (non-condensing). • Storage of reagents (Element 7: Equipment and Supplies)
Xpert MTB/RIF test reagents must
be stored at 2-28°C
6.2. Create and maintain a safe working environment
The main occupational biosafety risks at a testing site are related to the inhalation of aerosols containing
TB bacilli. The risk of infectious aerosol generation depends on:
• Type of procedure (e.g., splitting samples, vortexing, centrifugation)

• Frequency of testing and the testing site’s workload
• Consistency of the material and its predisposition to aerosolize (e.g., viscous versus non-viscous
liquids)
• Number of TB bacilli in the material or specimen (e.g., smear positive samples versus smear negative
samples)
WHO has adopted an approach that assesses the risks associated with different technical procedures
performed in different types of TB laboratories. WHO’s Tuberculosis laboratory biosafety manual
(2012)29 describes the minimum requirements for facilities and the safe working practices that can be
adopted following a risk assessment.
29 Tuberculosis Laboratory Biosafety Manual. WHO. 2011. (http://www.who.int/tb/publications/2012/tb_biosafety/en/)
52
Biosafety
When used with unprocessed sputum specimens, the Xpert MTB/RIF test is a low-risk procedure and
requires the same level of precaution as for performing direct AFB sputum-smear microscopy. When
appropriate microbiological techniques are used, direct smear testing and processing of specimens
for the Xpert MTB/RIF assay may both be carried out on an open bench in an adequately ventilated
area. The bench used to process specimens for these procedures should be separate from areas where
specimens are received and from areas where paperwork is completed and telephones are used.
Appropriate PPE must be used (see below).
In the WHO’s Tuberculosis Laboratory Biosafety Manual29, adequate ventilation is described as directional
airflow with 6–12 air exchanges per hour. For low-risk procedures such as Xpert MTB/RIF(2012),
natural ventilation should be sufficient providing that air flows away from the technician and across
the work area along with potentially infectious materials, then away from occupied areas of the room
and to outside the laboratory. When the climate or use of air conditioning prevents the use of natural
ventilation (e.g., from open windows), mechanical ventilation systems may be needed to provide an
inward flow of air without recirculation in the room, or the use of ventilated workstations or certified
biosafety cabinets may be needed to ensure a safe working environment. Note that the use of separate
rooms may allow for adequate (natural) ventilation in the area where specimens are processed and
cartridges are loaded and the use of air conditioning in the areas where the GeneXpert instrument is
located and where temperature-sensitive supplies and reagents are stored. As needed, consult with a
biosafety expert for a thorough analysis and recommendations.
Splitting or processing of specimens (e.g., NaLC-NaOH digestion and decontamination) are considered
moderate-risk activities for generating infectious aerosols and must be performed within a certified
Biological Safety Cabinet (BSC) and appropriate PPE must be used (see below).
Testing sites should conduct a risk assessment to determine whether additional safety precautions are
required, such as when performing the Xpert MTB/RIF test in settings with a high burden of MDR-TB or
when laboratory personnel are at increased risk of acquiring TB.
Personal Protective Equipment (PPE)
PPE minimizes the risk of exposure to aerosols, splashes and accidental inoculation. PPE includes
laboratory coats and gowns, gloves and respirators:
• Wearing gloves is recommended. However; it may give technicians a false sense of safety; regular
and thorough hand washing is essential. Gloves must be changed if they become contaminated or
compromised.
• Surgical masks are not respirators, and do not protect the wearer against inhaling infectious aerosols.
Surgical masks must not be worn in TB laboratories or testing sites.
• WHO does not recommend the use of respirators for sites only performing the Xpert MTB/RIF test
and smear microscopy (i.e., low-risk testing sites) in adequately ventilated laboratories. The use of
respirators does not replace the requirement for adequate ventilation. However, respirators must
be used in medium- and high-risk testing sites; when recommended by countries or facilities; when
testing samples from patients with high risk of MDR-TB; when splitting samples or when testing
decontaminated and concentrated samples.
29 Tuberculosis Laboratory Biosafety Manual. WHO. 2011. (http://www.who.int/tb/publications/2012/tb_biosafety/en/)
53
Waste management
Waste management procedures must comply with all pertinent local and national requirements and
regulations. All materials associated with the Xpert MTB/RIF test should be treated as if they are
biohazardous. All potentially infectious materials (except sharps) should be placed in properly labelled
disposable biohazard bags. The biohazard bags containing the contaminated material should be
sealed before being promptly transported for autoclaving or incineration. Transfer pipettes should be
decontaminated using an appropriate disinfectant prior to disposal (e.g., place used pipettes in a one-liter
plastic beaker containing 10% bleach solution and allow at least one-hour contact time before discarding
pipettes into biohazard plastic bags).
Correctly prepare disinfectants
The optimal working concentrations for common disinfectants used at testing sites are:
• Bleach: 0.5% final concentration of chlorine in water (e.g., mix 10 ml of 5% bleach solution with 90 ml
water), except for disinfecting transfer pipettes (see above).
• Alcohol: 70% solution
• Peracetic acid: 2% in water
Bleach and peracetic acid must be prepared daily. The working concentration of the bleach solution
is usually prepared by dilution of concentrated household bleach, which may vary between 3% and
5%. Laboratories must determine the appropriate dilution factor based on the household bleach
concentration. Laboratories must adhere to the manufacturer’s recommendation regarding expiry dates
and label prepared disinfectants with name, concentration, date prepared and expiry date.
54
Element 7. Equipment and supplies
7.1. Maintenance and calibration of the

GeneXpert instrument Activities at a glance
The GeneXpert is a precision instrument that requires

regular maintenance to ensure that it provides accurate Maintain all testing site
and precise results. The instrument is purchased with a equipment in a good working
24-month limited warranty. Extended warranties can be condition
purchased to cover the period after the warranty expires.
Maintenance contracts and service level agreements are Perform preventative
also available to ensure regular maintenance and service. maintenance
The GeneXpert instrument must be verified as functioning
properly before testing any clinical specimens. The Monitor instrument performance
GeneXpert instrument must be recalibrated according to and perform on-request
the manufacturer’s recommendations. Failure to maintain maintenance as required
the GeneXpert instrument can affect quality:
Ensure warranties and service
• Poorly maintained equipment is prone to failures, which contracts are in place and
result in delayed reporting, lack of access to services or adhered to
inaccurate Xpert MTB/RIF test results being reported
• Failure to ensure warranties or maintenance agreements Forecast how many cartridges
are adhered to can be costly if modules fail will be used and monitor Xpert
MTB/RIF cartridge consumption
What you need to do
Implement a stock control
7.1.1. Perform instrument verification system to manage Xpert MTB/
RIF stock
Each module in the GeneXpert instrument should be
evaluated as being “fit for purpose” through verification Store Xpert MTB/RIF
with known positive and/or negative material prior to cartridges in accordance with
commencing testing of clinical specimens. At least a manufacturer’s recommendation
single verification test should be performed per module
upon instrument installation and following calibration or
swapping of instrument modules. Verification panels are
routinely distributed by Cepheid with each new instrument and with re-calibrated modules. Additional
verification panels may be required if instruments are moved and would need to be ordered. These
verification panels consist of a card containing five dried culture spots (DCS) of a known concentration
of whole inactivated RIF-susceptible MTBC. 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.”
• If an invalid/error/no result is obtained on any module, repeat the test in that module using the extra
DCS sample provided.
• Instrument verification results should be reported to NTRL or the appropriate person responsible for
overseeing testing in the country and Cepheid should be contacted immediately in order to assist with
any issues encountered during verification process.
• The GeneXpert verification records must be kept at the testing site throughout the lifetime of the
instrument.
55
7.1.2. Maintain a functional GeneXpert Instrument
The GeneXpert is a precision instrument that requires regular preventative maintenance and ad hoc
servicing and maintenance.
Preventative maintenance should be performed on regular basis by the end-user to ensure good
performance of the GeneXpert instrument. Step-by-step procedures are described in the GeneXpert
User Manual. Preventative maintenance should be recorded on the GeneXpert Maintenance Log.
Maintenance records must be reviewed by the testing site manager at least monthly and during
supervisory visits and instrument-related problems followed-up.
On-request maintenance should be performed in specific situations upon request by Cepheid Technical
Support. It allows the checking or the re-setting of the instrument in case of malfunctioning. On-request
maintenance is recorded in the GeneXpert Maintenance Log.
7.1.3. Maintain warranty coverage
All GeneXpert systems, with the exception of the GeneXpert Infinity product line, come with a
24-month warranty on service and parts. Three and five-year warranty extensions can be purchased.
Warranties typically cover instrument or module repair and/or replacement. All shipment costs are
included. Not included are travel costs for all onsite interventions. Guidance on extended warranties
can be accessed from the FIND website (https://www.finddx.org/find-negotiated-product-pricing/). Programmes
should contact Cepheid or their Authorized Service Provider for details of the extended warranties and
quotes for the cost of the warranties and covered services. Alternatives to an extended warranty are
maintenance contracts and service level agreements.
7.1.4. Arrange for module repair and replacement
If a module failure is suspected, the testing site must initiate efforts to have the module repaired or
replaced. This may require supplying the Installation Qualification ( IQ) report and the error report to
the GeneXpert Focal person in country or directly to Cepheid depending on the country’s processes and
procedures. Cepheid will inform the testing site if the module needs replacing. The GeneXpert Focal
Person or implementing partner (if applicable) must be informed and copied on all correspondence if
Cepheid is contacted directly. Module replacement may take a few days to several months depending
on the reason for replacement, the partners involved (if applicable), the warranty and the location of the
instrument. An adequate budget for module repair and replacement must be available and promptly
disbursed when needed.
How do I ensure well-functioning GeneXpert instruments?
• Evaluate each module in the GeneXpert instrument for being “fit for purpose” through verification
with known positive and/or negative material prior to commencing testing of clinical specimens, after
service or calibration, or after moving instruments
• Perform routine maintenance according to the recommended daily, weekly and monthly schedules.
Records of maintenance must be kept
• Ensure GeneXpert instruments are recalibrated according to the manufacturer’s recommendations
• Monitor performance of each module (e.g., failed runs) and record in a maintenance log. Use
the capabilities of the diagnostic connectivity system to monitor the performance of GeneXpert
instruments and individual modules
• Obtain servicing and repair of instruments from authorized service providers according to national
policies, procedures and SOPs
• Purchase extended warranties or service contracts for each GeneXpert instrument
56
What you need to do
7.2. Ensure adequate supplies & reagents
A robust inventory system is required to monitor Xpert MTB/RIF cartridge consumption. Accurately
forecasting Xpert MTB/RIF test supply needs reduces the risk of an interruption in service due to
shortage of reagents. Failure to maintain an adequate, uninterrupted supply of quality-assured reagents
can affect quality because 1) stock-outs result in delayed testing and delayed reporting of results and 2)
use of poor quality or expired reagents can result in high error rates and inaccurate test results.
7.2.1. Manage Xpert reagent stock
Inventory management is the process of ordering, receiving and storing supplies to provide an
uninterrupted Xpert MTB/RIF test service.
1. A first step is to forecast how many Xpert MTB/RIF cartridges will be used in the period (e.g., one
month). To accurately forecast how many cartridges to purchase, the testing site must be aware of its
average usage, the lead time for delivery and the capacity for cold storage.
The average usage of Xpert MTB/RIF reagents can be calculated by reviewing the number of tests
performed per month. Lead time is defined as time between placing an order and receiving it at the
testing site. The lead time needs to consider the time taken to clear customs, and the transport time to
the testing site level.
Calculating how much to order:
a = number of Xpert MTB/RIF tests performed (e.g, 210 tests)

b = number of months (e.g, 3 months)
c = average usage per month (a ÷ b) (e.g, 210 ÷ 3 = 70 tests per month)
d = lead time (e.g, 4 months)
e = stock in-hand (e.g, 140 cartridges)
f = recommended buffer stock (2 months average usage = 140 tests)
Minimum Xpert MTB/RIF cartridges to order for a four-month lead time:
(c × d) – e + f = (70 × 4) – 80+140 = 340 cartridges
2. Monitor Xpert MTB/RIF cartridge consumption by using a supply management system (e.g., stock
cards or an electronic equivalent). Minimum order levels and lead times must be calculated and
documented on stock cards. Rotation of stock using “First-in, First-out” (FIFO) and First Expired, First
Out (FEFO) principles ensures that out of date reagents are not used. Forecasts should be reviewed and
updated from time to time based on actual consumption. Significant variations away from the average
monthly consumption should be accounted for to ensure uninterrupted supply of reagents.
3. Label all supplies and reagents with date received, the date first opened and new expiry date when
opened; where possible, limit stocks to a six-month supply.
57
7.2.2. Quality control of new batches of cartridges and reagents
New lot testing, also known as lot-to-lot verification, is performed on new batches of cartridges and
reagents. New lot testing usually consists of testing a sample of the new cartridges and comparing the
results to existing lot of cartridges with known performance:
• Conditions during transport & storage of cartridges may affect their performance.
• Cartridge test failures may indicate that the new batch of cartridges are not fit for use.
New lot testing is preferably performed at the central (e.g. NTRL) or regional level, thereby ensuring
that cartridges with test failures are not distributed and reducing the burden of testing and number of
cartridges used.
On occasion, new lot testing at the testing site may be needed to monitor conditions during transport
and storage of cartridges in-country or to meet ISO 15189 requirements for accreditation. In this case,
the use of positive and negative controls (e.g., PT samples, sputum or simulated samples of known
reactivity) is recommended for incoming QC of new batches of reagents. The results from positive
and negative controls must be recorded, and unexpected results must be recorded, investigated and
monitored for trends over time. QC records must have documented review by the testing site manager
and retained onsite for a period according to local or national policy. See Supporting Documents/forms
and templates for New lot testing SOP template.
7.2.3. Properly store cartridges and reagents
Adverse environmental conditions, outdated reagents, improper reagent shipment and improper
reagent storage are all possible sources of error that can invalidate the Xpert MTB/RIF test results. Xpert
MTB/RIF cartridges and reagents must be stored at 2-28°C. Expired reagents or cartridges must not
be used.
How do I ensure the quantity and quality of supplies?
• Manage supply of Xpert MTB/RIF cartridges (forecast needs and order in a timely manner) to provide
an uninterrupted Xpert MTB/RIF testing service
• Conduct new lot testing on each new batch of cartridges as needed
• Properly store Xpert MTB/RIF cartridges and monitor expiration dates
58
Element 8. Participate in an EQA programme
Testing sites should participate in an EQA program that

includes proficiency testing, on-site evaluations and Activities at a glance
supportive supervision. The Xpert MTB/RIF Proficiency
Testing (PT) programme is an important tool for
communicating with and motivating staff. Used correctly, Enroll the testing site in an Xpert
the PT programme can be used to identify and resolve MTB/RIF PT programme
problems in Xpert MTB/RIF testing. On-site evaluations
and supportive supervision can facilitate evaluation of the Perform PT testing as required.
quality of testing, analyse QA results, identify problems, Receive and analyse PT reports.
provide corrective actions and document improvements.
Failure to enroll in a comprehensive EQA program, is a Troubleshoot unexpected PT
missed opportunity to identify and correct problems that results and identify corrective
affect the quality of testing. actions
What you need to do Participate in a system of

supportive supervision and on-
8.1. Participate in a system of supportive supervision site evaluations
and on-site evaluations
On-site supportive supervisory visits for assessments

and training are especially critical during early stages of implementing a new test or procedure as they
provide motivation and support to staff. On-site supervisory visits are also good opportunities to provide
refresher training, mentoring, troubleshooting advice and technical updates. Strong relationships
with GeneXpert users encourage rapid reporting of any problems and enables rapid troubleshooting,
re-training and corrective actions. In addition to providing constructive feedback on performance,
supportive supervision provides updates on technical guidelines and procedures, opportunities
for training and assistance with reviews of quality indicators and results of PT and development of
corrective actions.
Given the large benefit of supportive supervision on the quality of laboratory testing, testing sites should
proactively seek out opportunities to participate in a system of supportive supervision by contacting
supervisory laboratories, QA assurance focal points at the regional or national level, the TB programme
officers or Xpert implementing partners.
In most settings, the NTRL or supervisory laboratory will be responsible for planning and conducting
the on-site evaluations. The supervisory visits should be planned at regular intervals with schedules
communicated to sites in advance. The on-site evaluations should use standardized checklists and
include discussions with GeneXpert users, testing site management, review of Xpert MTB/RIF test
site documentation and observation of testing site operations. Any problems identified during the
assessment should be discussed immediately with facility staff and a plan established for addressing
problems. The testing site should receive interim feedback immediately after the supervisory assessment
and subsequently a full supervision report. The testing site should undertake and document any
recommended corrective actions in a timely manner.
59
How do I participate in a site supervisory programme (Testing Site)?
• Schedule supervisory visits according to national policy

• Prepare necessary documents for supervisory visits
• Undertake and document any recommended corrective actions
8.2. Testing PT panels
The objective of PT is to ensure inter-testing site comparability of results. The Xpert MTB/RIF test
results reported by each testing site are compared to the reference laboratory Xpert MTB/RIF test result.
All testing sites should enroll in an Xpert MTB/RIF PT programme. The GeneXpert Focal Person or the
QA Unit can facilitate participation in the PT program.
The National program will decide which PT panels to use. A variety of PT panels using different sample
matrices were evaluated by Scott, et al in 2014 and found to be equivalent. Included in this evaluation
were artificial sputum (WHO/GLI), dried tube specimens (CDC), dried culture spots (National Health
Laboratory Service (NHLS), South Africa) and two commercial suppliers (lyophilized samples and liquid
samples). Currently, PT panels are available from CDC (for selected countries and sites), Smartspot
Quality (South Africa) and INSTAND Germany (MMQCI). Alternatively, a country may elect to prepare
and use its own PT panels, see SOP templates in the Supporting Documents/forms and templates. PT
panels should preferably be tested quarterly.
The PT programme assesses pre-analytical, analytical, and post-analytical processes occurring at the
testing site, and not necessarily each GeneXpert module. PT panels should preferably be tested quarterly.
Module functionality should be verified using the Xpert Check.
Pre-analytical
–– Assess that the contact details of the testing site correspond with those on record at the PT programme
provider
–– Store the PT panels in accordance with the instructions provided with each panel
Analytical
–– Follow the instructions for preparing the sample for testing as directed by the PT programme provider
–– Perform the Xpert MTB/RIF test as you would a routine patient specimen
Post-analytical
–– Record the result of the Xpert MTB/RIF test on the report form provided by the PT programme
provider
–– Report the results to the PT programme provider and to the GeneXpert Focal Person or QA Unit (if
required)
–– The PT panel results will be analysed and compared to the expected results. The results will be scored
and the outcome reported to the testing site and the QA Unit
–– Review the outcome of the PT testing report
–– If there are any PT failures, troubleshoot (e.g., using root-cause analysis) and perform corrective
actions
How do I participate in a PT programme (Testing Site)?
• Enroll in an Xpert MTB/RIF PT programme in accordance with national policies and procedures
• Perform PT testing as required. Receive and analyse PT reports
• Troubleshoot unexpected PT results and identify corrective actions
• Undertake and document any corrective actions
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Element 9. Monitor and analyse Xpert MTB/RIF quality indicators
Testing sites should participate in an EQA program that

includes proficiency testing, on-site evaluations, and Activities at a glance
supportive supervision. The Xpert MTB/RIF Proficiency
Testing (PT) programme is an important tool for
communicating with and motivating staff. Used correctly, Implement quality indicator
the PT programme can be used to identify and resolve monitoring
problems in Xpert MTB/RIF testing. On-site evaluations
and supportive supervision can facilitate evaluation of the Regularly review quality
quality of testing, analyse QA results, identify problems, indicators and troubleshoot
provide corrective actions, and document improvements. unexpected results by
Failure to enroll in a comprehensive EQA program, is a identifying corrective actions
missed opportunity to identify and correct problems that
affect the quality of testing. Report quality indicator data to
the NTP/MOH
What you need to do
9.1. Identify and implement quality indicator monitoring
In most cases, the NTRL or supervisory laboratory will determine which indicators (See Element 9 of
Part 1) are to be monitored, analysed and reported by each Xpert MTB/RIF testing site as well as the
thresholds or targets for indicators (e.g., the Xpert MTB/RIF test error rate should be less than < 3%).
The testing site manager will need to develop or obtain forms to collect the data for each indicator,
train personnel in the importance and use of the indicator data collection forms, implement the routine
collection of indicator data and use the data to inform action plans for improvement.
Table 14 lists GLI recommended key performance indicators for Xpert MTB/RIF testing as well as
general laboratory quality indicators30 that should be monitored monthly by each testing site. Additional
indicators such as the completeness of documentation (e.g., use and completeness of registers, logs,
forms) or adherence to SOPs may be assessed during supervisory visits. For some indicators (e.g.,
proportion of specimens that are rifampicin resistant), targets are setting-specific. Laboratories should
monitor indicators and establish local targets and acceptable ranges. Deviations from expected values
should be investigated.
Sites should collect disaggregated data according to the population group tested (e.g., HIV positive,
MDR-TB risk, extrapulmonary TB). If the quality indicator for error rates exceeds the target value, it
should be further disaggregated to identify common error codes, in order to assist with corrective and
preventive actions. The GeneXpert platform produces electronic data, and therefore a data connectivity
solution should be established to enable remote monitoring of quality indicators (see Element 5).
30 GLI Practical Guide to TB Laboratory Strengthening. 2017. Available at http://stoptb.org/wg/gli/gat.asp.
61
Table 14. Key performance indicators that should be monitored monthly by testing sites
Xpert MTB/RIF Testing Quality Indicator Target
Number of tests performed, by type of test and key Full utilization of a 4-module GeneXpert instrument is
population (e.g., HIV+, previously treated) 12 tests per workday.
Service interruptions (stock-outs, equipment down

No interruptions
time, etc.)
detected, rifampicin resistance not detected resistance prevalence and patterns
detected, rifampicin resistance detected resistance prevalence and patterns
Number and proportion of specimens with MTBC Dependent on population tested and country drug
detected rifampicin indeterminate resistance prevalence and patterns
Number and proportion of specimens with MTB

Dependent on population tested and country drug
detected trace, disaggregated by patient group (For
resistance prevalence and patterns
Ultra test)
Number and proportion of specimens with MTBC not Dependent on population tested and country drug-
detected resistance prevalence and patterns
Number and proportion of specimens with errors <3%
Number and proportion of specimens with invalid

<1%
results
Number and proportion of specimens with no results <1%
Proportion of specimens tested with Xpert MTB/RIF

>95%. The target turnaround time may be modified by
for which a result was reported within 24 hrs (i.e., time
the programme based on testing schedules
from receipt of specimen to reporting of results)
In addition to the indicators of the quality and performance of the Xpert MTB/RIF testing, sites may be
requested by the NTP to collect and report data for additional indicators needed to assess the quality of
the diagnostic cascade or to assess aspects of laboratory strengthening under the End TB Strategy. The
national or supervisory level will determine the frequency of collection of these data (e.g., once or twice
a year).
62
Table 15. Key performance indicators to monitor the quality of the diagnostic cascade
Number and percentage of presumptive TB patients

Dependent on population tested and country
tested with Xpert MTB/RIF (End TB Strategy
prevalence patterns
Laboratory Indicator 1)31
Percentage of notified new and relapse TB cases tested

80% (2020)
with a WRD as the initial diagnostic test (Indicator 2)
Percentage of notified new and relapse TB cases with

80% [relapse: 90%] (2020)
bacteriological confirmation (Indicator 3)
Number and proportion of bacteriologically confirmed

patients who were initiated on treatment according to Target is setting specific
the national algorithm
Percentage of testing sites using a WRD at which a data

connectivity system has been established that transmits
100% (2020)
results electronically to clinicians and to an information
management system (Indicator 4)
Number and proportion of Xpert MTB/RIF test results

reported to clinicians using electronic systems
Number and proportion of TB patients detected by

Xpert MTB/RIF that were reported to the TB control Target is setting specific
program, TB or MDR TB treatment focal person
Percentage of notified bacteriologically confirmed TB

100% (2020)
cases with DST results for rifampicin (Indicator 7)
Percentage of notified rifampicin-resistant TB cases

with DST results for fluoroquinolones and second-line 100% (2020)
injectable agents (Indicator 8)
Number and proportion of patients with RIF-resistant

TB identified by Xpert MTB/RIF testing referred for 100%
second-line DST
Proportion of specimens collected for Xpert MTB/ >95%. The ‘specified time’ should be determined for
RIF testing for which a result was received within the each laboratory taking into account testing schedules
specified target time (i.e., time from collection of a and specimen transport schedules (e.g., on demand,
specimen to receipt of results) daily, twice weekly, etc.)
>95%. The ‘specified time’ should be determined for

Proportion of specimens referred for DST for which a
each test required (e.g., molecular DST or liquid culture
result was received within the specified target time (i.e.,
DST) and the collection schedule used (e.g., on demand,
time from referral of a specimen to receipt of results)
daily, twice weekly, etc.)
31 The indicator number in parentheses refers to the number of the global indicators in the WHO Framework of indicators and targets for laboratory
strengthening under the End TB Strategy. Available at http://www.who.int/tb/publications/labindicators/en/
63
9.2. Regularly review quality indicators and troubleshoot unexpected results by identifying
corrective actions
All laboratories should collect and analyse performance data on at least a monthly basis, using a
standardised format. Examples of data collection and analysis forms for key performance indicators
as Microsoft Word files and in an Excel format that can automatically calculate the indicators when the
required data are entered.
Targets should be set for all indicators monitored (usually set by the national or supervisory levels), and
any unexplained change in quality indicators, such as increase in error rates, a change in MTB positivity
rate or RIF-resistance rate, or a significant change in volume of tests conducted, should be documented
and investigated. Indicators should be reviewed by the laboratory manager and must always be linked to
corrective actions if any unexpected results or trends are observed. Documentation of corrective actions
and subsequent improvement and normalization of laboratory indicators following the corrective
actions are critical.
A system should be in place for reporting of monthly quality indicators to the supervisory laboratory,
NTR or NTP. These data should also be made available to the supervisory laboratory prior to
supervisory visits to facilitate analysis and development of corrective actions if necessary. For Xpert
MTB/RIF testing, the use of diagnostics connectivity solutions (Element 5) will allow for real-time
remote monitoring of sites within a network and provide the capacity to easily and accurately stratify
data as needed for analysis of performance.
An example of Xpert MTB/RIF test performance indicator data collected and analysed at a testing site is
shown below:
Figure 4: Performance Indicator - Number of Xpert MTB/RIF Test Errors

25
20
At this testing site, there is an

increase in the number of Xpert
15 MTB/RIF test errors between
January and April (9, 12, 15 and 21
respectively).
10
Increases in the number of Xpert
MTB/RIF test errors suggests that
routine maintenance is not regularly
5
being performed. Also, if a particular
module produces more errors over
time as compared to the other
0 modules, it may require repair.
Jan Feb Mar Apr
What should be done?
Perform a root cause analysis:

• Example 1: the test errors are associated with one module, error code 5007. Solution: the module
must be replaced.
• Example 2: the test errors are associated with a particular user. Solution: the user must be retrained.
64
9.3. Report quality indicator data to the NTP/MO
QA and quality improvement are a continuous and cyclical process. Data should be collected and initially
reviewed at the local testing site level. Trends that require intervention (e.g., increase in proportion of
unsuccessful results, increase in service interruption) must be communicated, appropriate corrective
actions must be undertaken and impact of the interventions reviewed. As far as possible, sites should
be empowered to analyse their own data in order to be able to take corrective actions without external
assistance. However, more complex issues (e.g., an increase in rifampicin-resistance) may need support
from higher levels (e.g., supervisors, advanced GeneXpert users) in order to recommend appropriate
actions.
Furthermore, the monthly reports of performance indicators will be collated and analysed at the
regional and national levels to identify trends that extend beyond individual sites (e.g., reagent batch
issues, PT, or equipment maintenance). The results of these analyses should be communicated to the
sites so that they may take corrective action as needed.
65
Element 10. Strengthen the clinical-laboratory interface
and the diagnostic cascade
A comprehensive system to ensure the quality of

laboratory testing must address all the relevant parts Activities at a glance
of the diagnostic cascade, not just what happens in
the laboratory. Published literature on a variety of
laboratory tests highlights that factors that have the Provide training on the
largest impact on quality of diagnostic services occur diagnostic cascade to all
in the pre-pre-analytical phase (choice of test, etc.) and laboratorians and healthcare
post-post-analytical (interpretation of results and patient workers
management).
Collect and test quality samples
Key steps in strengthening the clinical-laboratory interface
and assuring the quality of the diagnostic cascade that the Report accurate results
testing site can do include:
• provide training to laboratorians, nurses, clinicians and

other healthcare workers on the aspects of the diagnostic cascade that affect the quality of TB testing
(e.g., collecting quality specimens)
• collect quality samples and promptly submit to the testing site along with a properly completed test
requisition form
• report accurate results to clinicians, TB control officers and TB and MDR TB treatment focal persons
and include information on the interpretation of the test results
10.1. Provide training on the diagnostic cascade to laboratorians and health care workers
A standardized training programme should be available from the NTP or NTRL and include training
curricula for laboratorians, nurses, clinicians and other healthcare workers on the aspects of the
diagnostic cascade that affect the quality of TB testing. Testing sites should keep a log of trained staff
and those requiring training and interact with appropriate authorities to have staff trained. All training
should be documented, with plans made for regular refresher trainings. Regular meetings can be used to
impart information to laboratory and facility staff on updates to procedures and processes.
• The GLI standardized curriculum for Xpert MTB/RIF users and advanced users contains modules that
address the diagnostic cascade.
• Clinical trainings should be conducted as part of the continuous medical education of healthcare
and clinical staff. Testing site managers may be required to provide training to familiarise staff from
referring sites on the uses and limitations of the Xpert MTB/RIF assay and provide training on
ordering of tests, completion of request forms and interpretation of test results. This will help ensure
that national testing algorithms are followed, the correct test is ordered for each patient, quality
samples are collected and submitted to the laboratory, accurate results are reported to the clinician,
results are correctly interpreted and patients are promptly placed on appropriate therapy.
66
10.2. Test quality samples
Activities at a glance
A good quality specimen is required to produce a quality
Xpert MTB/RIF test result. Specimens must be properly
collected, labelled, stored and promptly transported to Inform healthcare workers on
the testing site. Standardized test requisition forms must the sample requirements for
be used and completely filled out with all the required Xpert MTB/RIF testing
information. Failure to obtain and use good quality
specimens can affect quality because Ensure patients are instructed
in good sputum collection
• Specimens may be rejected because of poor quality, technique
inadequate volume or improper labelling which may
lead to recalling patients to obtain a good quality Ensure complete and accurate
specimen which may lead to a delay in diagnosis labelling of specimen containers
• The use of poor quality specimens may lead to high and request forms
error rates and wastage of cartridges and supplies
• Incomplete or incorrect labelling may lead to inaccurate, Establish clear policies and
misdirected or delayed reporting. procedures for sample rejection
What you need to do
10.2.1. Collect good quality sputum samples
Good quality specimens are essential to achieve good quality test results. Sputum specimens must:
• Have adequate volume. A minimum of 1ml of sputum is required for the Xpert MTB/RIF test.
• Be of good quality. A sputum specimen must be from the lungs, not from the nose and mouth. If the
sputum is too bloody or contains too much pus, or food particles, it may cause an invalid Xpert MTB/
RIF test result.
The Xpert MTB/RIF test can also be used for the detection of MTBC in certain non-respiratory
specimens (e.g., cerebrospinal fluid, lymph nodes and other tissues), which are usually collected in higher
level facilities. SOPs for processing these samples can be found in the Xpert MTB/RIF implementation
manual - Technical and operational ‘how-to’: practical considerations32. Clinicians should refer to accepted
local and international standards for the collection of these samples. Specific requirements for non-
respiratory specimens are:
• For cerebrospinal fluid, a minimum volume of 0.1ml is required for the Xpert MTB/RIF test.
• Lymph nodes and other tissues must be processed in a BSC given the risk of producing aerosols while
grinding and homogenizing samples.
Sputum must be collected in a durable, screw top, plastic container. Ensure that SOPs on how to collect
good quality sputum samples are available on site and that patients are instructed in providing good
quality specimens. The Laboratory Diagnosis of Tuberculosis by Sputum Microscopy - The GLI Handbook33
contains useful guidance on collecting sputum samples for the diagnosis of TB.
32 Xpert MTB/RIF implementation manual - Technical and operational ‘how-to’: practical considerations. http://who.int/tb/publications/xpert_im-
plem_manual/en/
33 Laboratory Diagnosis of Tuberculosis by Sputum Microscopy - The GLI Handbook. GLI. 2013. http://www.stoptb.org/wg/gli/gat.asp
67
10.2.2. Store and transport specimens
If specimens are not collected on site, it may be necessary to store specimens at the collection site until
they can be transported to the Xpert MTB/RIF testing site. Procedures and considerations for storing
and transporting TB specimens may be found in the GLI Guide for TB Specimen Referral Systems and
Integrated networks34.
Process and Considerations How do I achieve this?
Storage • After specimen collection, store the sputum container in a

• If there is a delay in sending sputum samples fridge/cooler box (do NOT freeze) until collection for transport
to the testing site, they should be stored at to the testing site
2-8°C prior to transport • For Xpert MTB/RIF testing, bacteria in the sputum specimens
• Samples may be stored at 2-8°C for a can be inactivated and then stored and transported at ambient
maximum of 10 days prior to testing temperature or at 2–8°C35.
• Samples may be stored at a maximum of • Protect the sputum container against heat and sunlight and
35°C for up to 3 days, and then refrigerated at place the container in a plastic bag to prevent contamination
2-8°C for a combined maximum duration of • Keep a record of sputum collection at the clinical facility, and
10 days the date of transport to the testing site
• Samples must be transported in such a way as to prevent

spillage or leakage while in transit.
Specimen transport • Triple packaging must be used.
• Sputum samples should be transported to the • Drivers of vehicles transporting sputum should be educated
testing site as soon as possible, preferably on regarding safety procedures and have access to a spill kit in case
the day of collection of a spill or leakage
• A specimen transport log should be used to track specimen
transport
• Upon receipt of samples, ensure that the request forms are

completed and that the samples are correctly labelled
• Record the date and time that specimens arrive at the testing
Specimen receipt
site. The testing site should monitor specimen transport times to
• Sputum samples must be promptly
troubleshoot delays if they occur
processed at the testing site
• The testing site must evaluate and record the quality and
volume of sputum samples. Report back to referring facilities in
case of poor quality specimens or incomplete labelling
10.2.3. Sample rejection
Testing sites should have a policy for rejecting samples for Xpert MTB/RIF testing. The policy must be
communicated to clinicians and healthcare workers requesting Xpert MTB/RIF testing. Records should
be kept of the number of rejected samples. If a sample is rejected, the testing site must attempt to collect
another sample. Reasons for rejecting samples include:
• The sample is incorrectly labelled or is received without the necessary requisition forms - these
samples may not correctly identify the patient;
• The sample has leaked in transit - these samples are a risk to testing site personnel;
• In case of sputum, the volume is less than 1ml or the sputum is too bloody and/or contains too much
pus - these samples may give erroneous results.
34 Guide to TB Specimen Referral Systems and Integrated Networks. GLI. 2017. http://www.stoptb.org/wg/gli/gat.asp
35 Technical Expert Group Meeting Report: Commercial sample transport products. Geneva, World Health Organization. 2017. (WHO/HTM/
TB/2017.19). http://www.who.int/tb/areas-of-work/laboratory/policy_statements/
68
10.3. Report accurate results
Activities at a glance
The Xpert MTB/RIF test results produce reports indicating
whether the sample contains MTBC and whether MTBC
is resistant to RIF. Test results must be reported as soon as Inform healthcare workers on
possible to allow rapid treatment initiation. Standardized the sample requirements for
test report forms must be used that contain all the Xpert MTB/RIF testing
required information on the test result and interpretation.
Inaccurate reporting of results can lead to under- or over- Ensure patients are instructed
diagnosis of TB or drug resistance, leading to negative in good sputum collection
impact on patients and the community. The lack of technique
standardization of reporting may lead to confusion and
incorrect interpretation of results. Ensure complete and accurate
labelling of specimen containers
What you need to do and request forms
10.3.1. Monitor performance of internal quality controls Establish clear policies and
procedures for sample rejection
Internal quality controls should be monitored for all tests
to ensure a quality result. Each Xpert MTB/RIF cartridge
contains a Sample Processing Control (SPC, non-infectious
lyophilized spores of Bacillus globigii) that verifies that proper lysis of MTBC has occurred, verifies
adequate processing of the specimen, and detects specimen-associated PCR inhibitor36. The SPC must be
positive in a sample where “MTB Not detected” and can be either positive or negative if “MTB Detected”.
If the control is negative in a “negative” sample, the test is “Invalid”.
Each Xpert MTB/RIF test cartridge also contains Probe Check Control (PCC). The PCC is a check
undertaken by the system before the start of the PCR reaction and measures the fluorescence signal
from the probes to monitor bead rehydration, reaction-tube filling, probe integrity and fluorescent dye
stability. If the PCC is not passed, the test is stopped, and an “Error” result is obtained.
36 GeneXpert Dx Systems Operator Manual. ftp://hbdc:[email protected]/
69
Probe Check
Test Stopped No Value

Pass Fail
At least 2 probes Pos Error
Yes
No
SPC
NB probes Pos
Pos Non Value
All 1 Neg or
positives more Neg Negative Invalid
MTB Detected MTB Detected
RIF resistance RIF resistance

not Detected Detected
Note that the use of external positive and negative controls with each Xpert MTB/RIF test run is not
feasible as each module (and each cartridge) is a single instrument. Xpert MTB/RIF test internal controls
are sufficient.
70
10.3.2. Report results
When performing the Xpert MTB/RIF test, the GeneXpert instrument reports whether the sample
contains MTBC (through the detection of DNA from MTBC) and whether MTBC is resistant to RIF
(through the detection of mutation in the rpoB hot-spot region). The MTB/RIF assay reports results as
MTB not detected; MTB detected RIF resistance not detected; MTB detected RIF indeterminate; MTB
detected RIF resistance detected, or error/no result/invalid. The MTB/RIF Ultra assay uses the same
semi-quantitative categories used in the Xpert MTB/RIF assay (MTB detected high, medium, low, and
very low) and adds a new semi-quantitative category, ‘MTB detected trace’. There is no information on
rifampicin resistance or susceptibility for samples with an MTB detected trace result.
If the Xpert MTB/RIF test is invalid, the GeneXpert instrument reports an error, invalid result or no
result. There are a number of reasons for an invalid result, including internal control failure due to the
presence of PCR inhibitors (pus, blood or food particles present in the sputum specimen) or failure of
the instrument due to electrical failure.
Xpert MTB/RIF results must be recorded in a standard format in the register (or equivalent, e.g.,
Laboratory Management System [LMS]) at the testing site. Xpert MTB/RIF results must be analysed
and reviewed on monthly basis to detect changes, which may indicate procedural problems (Element 9:
Monitor and analyse performance indicators).
The results of the Xpert MTB/RIF test are reported on the approved reporting form. Report Xpert
MTB/RIF results within 24 hours after the sputum specimen is received at the testing site to allow rapid
treatment initiation. Reports may be sent by Short Message Service (SMS), email or fax and can also
be sent as paper copies by courier, according to the arrangement with the referring sites (and national
policy). See Element 5 for a discussion of the uses of diagnostics connectivity systems for reporting.
Appropriate results reporting systems should be put in place to ensure rapid reporting of results to the
referring sites.
The report form should include additional information to assist the clinician in interpreting the results.
Details of testing Xpert MTB/RIF testing algorithms and interpretation of results are provided in the
GLI Model TB Diagnostic Algorithms37 and the GLI Guide on Planning for country transition to Xpert®
MTB/RIF Ultra Cartridges38.
Testing sites may need to update registers and reporting forms to comply with national policy.
37 GLI Model TB Diagnostic Algorithms. 2017. http://stoptb.org/wg/gli/assets/documents/GLI_algorithms.pdf

38 GLI Guide on Planning for country transition to Xpert® MTB/RIF Ultra Cartridges. 2017. http://www.stoptb.org/wg/gli/assets/documents/GLI_ultra.pdf.
71
Table 16: WHO recommended format for reporting Xpert MTB/RIF test results
Xpert MTB/RIF test result WHO reporting code
MTB not detected N
MTB detected RIF resistance not detected T
MTB detected – Trace (Ultra test only) TT
MTB detected RIF indeterminate TI
MTB detected RIF resistance detected RR
Error / No result / Invalid I
10.3.3. Protect data confidentiality
The data stored on the computer/laptop connected to the GeneXpert instrument contains sensitive
patient information, (i.e., name, patient ID and test results). Measures must be put in place to prevent
unauthorized access of data and data theft. Unauthorized access of data from the computer or laptop
(e.g., printing, copying of files to USB or CD) should be prevented by protecting the data (restrict network
and system access, enforce user authentication and requiring the use of unique, strong passwords by all
system users). Unauthorized access of data via an internet connection should be prevented by the use
of firewalls, limiting access to authorized users, maintaining antivirus software, and performing regular
system updates.
See the GLI Quick Guide to TB Diagnostics Connectivity Solutions39 for a discussion of data confidentiality
and security when using a diagnostics connectivity system.
39 GLI Quick Guide to TB Diagnostics Connectivity Solutions. GLI. 2016. http://stoptb.org/wg/gli/gat.asp.
72
Additional Resources
WHO Laboratory Quality Management System: handbook (2011). A comprehensive reference on laboratory
quality management systems and quality systems essentials for all stakeholders in health laboratory processes, from
management and administration, to bench- work laboratorians. The handbook covers topics that are essential for
quality management of a public health or clinical laboratory. (http://www.who.int/ihr/publications/lqms/en/)
GLI Training Package on Xpert MTB/RIF. The package consists of slide presentations that can be customized and
used to train GeneXpert users in all aspects of Xpert MTB/RIF deployment, including related QA procedures. Topics
covered include: Overview of TB and diagnostics, biosafety, specimen collection, procurement, installation, Xpert
MTB/RIF technology, results interpretation, reporting, troubleshooting, maintenance, a clinical guide, and quality
assurance. (http://stoptb.org/wg/gli/TrainingPackage_XPERT_MTB_RIF.asp)
Xpert MTB/RIF test training for healthcare workers. The training is based on WHO recommendations and provides
practical tools for implementing Xpert MTB/RIF testing. (http://www.finddx.org/tb/)
GLI Training Package: Programme Modules for Diagnostic Network Strengthening (2018). This modular training
package has been developed to guide programme and laboratory managers and their implementation partners on key
topics for diagnostic network strengthening. (http://www.stoptb.org/wg/gli/TrainingPackage_Programme.asp)
Roadmap for Xpert MTB/RIF implementation (2017). A schematic representation of the elements that are required
to implement quality assurance activities for the Xpert MTB/RIF test. (http://www.finddx.org/tb/)
Challenge TB Tools. Extensive library of TB laboratory tools, guidelines and manuals. (http://www.challengetb.org/
library/lab)
FIND TB laboratory strengthening resources. Free, generic SOPs, documents and forms can be customized for use at
testing sites. (https://www.finddx.org/implementation-resources/#tb)
GeneXpert Dx Systems Operator Manual. Instructions on how to operate GeneXpert® Dx System. (ftp://
hbdc:[email protected]/)
Xpert MTB/RIF implementation manual - Technical and operational ‘how-to’: practical considerations (2014).
This edition of the implementation manual replaces the first edition and takes into consideration the current body of
evidence and operational experiences available, in the context of the updated policy recommendations, including use
of Xpert MTB/RIF to diagnose pulmonary TB, paediatric TB, extrapulmonary TB and RIF resistance. (http:/who.int/tb/
publications/xpert_implem_manual/en/)
WHO Meeting Report of a Technical Expert Consultation: Non-inferiority analysis of Xpert MTB/RIF Ultra
compared to Xpert MTB/RIF (2017). The current WHO recommendations for the use of Xpert MTB/RIF now also
apply to the use of Ultra as the initial diagnostic test for all adults and children with signs and symptoms of TB and
in the testing of selected extrapulmonary specimens (CSF, lymph nodes and tissue specimens). (http://www.who.int/tb/
publications/2017/XpertUltra/en/)
GLI Guide on Planning for country transition to Xpert® MTB/RIF Ultra Cartridges (2017). Practical guidance for
planning and implementing a smooth transition from use of Xpert MTB/RIF to Xpert MTB/RIF Ultra cartridges.
Includes advice on how to develop an actionable implementation plan, from country-level to site-level, for adoption
of the Xpert MTB/RIF Ultra cartridge. (http://www.stoptb.org/wg/gli/assets/documents/GLI_ultra.pdf)
GLI Model TB Diagnostic Algorithms (2017). Model algorithms that graphically depict the most up-to-date WHO
recommendations on use of TB diagnostics and provides guidance on the interpretation of test results and follow-up
testing. (http://stoptb.org/wg/gli/assets/documents/GLI_algorithms.pdf)
GLI Quick Guide to TB Diagnostics Connectivity Solutions (2016). An overview of diagnostics connectivity solutions,
and what is required to establish one and use it effectively (http://www.stoptb.org/wg/gli/gat.asp). Also contains a link to
an online table comparing the functionalities of currently available software (http://tinyurl.com/gliconnectivity).
GLI Practical Guide to TB Laboratory Strengthening (2017). Practical guidance on implementation of WHO
recommendations and international best practices for TB laboratory strengthening. It is an updated version of the
GLI Guide for Providing Technical Support to TB Laboratories, providing the latest practical guidance on use of
newly recommended diagnostics in model algorithms, as well as guidance in key technical areas, including quality
assurance and quality management systems, specimen collection and registration, procurement and supply-chain
management, diagnostics connectivity, biosafety, data management, human resources, strategic planning and other
topics. (http://stoptb.org/wg/gli/gat.asp)
73
GLI Guide to TB Specimen Referral Systems and Integrated Networks (2017). This guide describes the various
phases to create and strengthen specimen referral systems, essential components involved in referral, as well as other
considerations for TB programme and laboratory managers, ministry of health officials, and other stakeholders
across disease programmes. In addition to describing transport mechanisms and equipment required to safely move
specimens, this guide also provides information on logistics, results reporting, data management, monitoring and
evaluation, and standard operating procedures that will facilitate and improve specimen referral systems.
(http://www.stoptb.org/wg/gli/gat.asp)
Laboratory Diagnosis of Tuberculosis by Sputum Microscopy–The GLI Handbook (2013). The handbook contains
useful guidance on collecting sputum samples and conducting AFB-smear microscopy for the diagnosis of TB. (http://
www.stoptb.org/wg/gli/gat.asp)
WHO Definitions and Reporting Framework for Tuberculosis–2013 revision (2014). Revised WHO standard
case definitions for TB and drug-resistant TB, the categories used to assign outcomes, and the standard reporting
framework for TB. (http://apps.who.int/iris/bitstream/10665/79199/1/9789241505345_eng.pdf?ua=1)
WHO Framework of indicators and targets for laboratory strengthening under the End TB Strategy (2016).
Collaborative strategy between between the WHO Global TB Programme and the GLI core group, that comprises 12
core indicators that measure countries’ capacity to detect TB accurately and rapidly using new diagnostics, provide
universal DST, and ensure the quality of testing. (http://www.who.int/tb/publications/labindicators/en/)
WHO Tuberculosis Laboratory Biosafety Manual (2012). The minimum biosafety measures that should be
implemented at the different levels of TB testing laboratories to reduce the risk of a testing site-acquired infection.
(http://www.who.int/tb/publications/2012/tb_biosafety/en/)
WHO Laboratory Biosafety Manual (2004). Helpful reference and guide for developing and establishing
national codes of practice for securing microbiological assets, ensuring their availability for clinical, research and
epidemiological purposes. (http://www.who.int/csr/resources/publications/biosafety/WHO_CDS_CSR_LYO_2004_11/en/)
TB Laboratory Biosafety Training (2014). This free, interactive Biosafety training course addresses the needs of TB
laboratories in low- resource settings by providing the tools needed to improve safety in the testing site. (https://www.
finddx.org/online-trainings/)
Providing Uninterrupted Power for GeneXpert® in Low and Middle Income Settings: A Practical Guide
(2017). Practical information on approaches and equipment for ensuring an uninterrupted power supply (UPS)
for GeneXpert instruments. (https://www.finddx.org/wp-content/uploads/2018/02/UPS-guide-XpertMTB-RIF_
FINAL_07DEC16.pdf)
Tuberculosis Laboratory Maintenance Plan (LMP) for preventive and routine maintenance of laboratory
equipment. Expert opinion of the European TB Laboratory Initiative 2017. Provides practical guidance for planning
and implementing equipment maintenance in TB laboratories in the WHO European Region. (http://www.euro.who.
int/__data/assets/pdf_file/0009/355788/WHO-ELI-TB-Lab-Maintenance-Plan_ENG.PDF)
Guidelines for Managing the Laboratory Supply Chain: Version 2. Arlington, Va.: USAID | DELIVER PROJECT, Task
Order 1 2008. General guidance for managing a laboratory’s commodities and describes planning, coordination, and
the well-recognized cycles of selection, procurement, distribution, and use. (http://deliver.jsi.com/dlvr_content/resources/
allpubs/guidelines/GuidManaLabSC_v2.pdf)
74
List of Supporting Documents/
Forms and templates
Link: www.stoptb.org/wg/gli/xpertqaguide.asp
1. Xpert MTB/RIF Quality Assurance Situational Analysis Checklist

Includes checklist for conducting a situational analysis of the status of Xpert MTB/RIF testing and quality assurance
activities. Part A addresses activities at the national and supervisory levels and Part B addresses activities at the
testing site level. An example of a portion of a completed situational analysis report is also provided.
Maintenance log template

Provides an example of a form to record maintenance
(https://www.finddx.org/implementation-resources/?level0=main-accordion-4&level1=secondary-left-accordion-1)
2. Indicator report forms

Contains forms as customizable MS Word files for collecting data for performance indicators and for calculating
the indicators. These forms are also available as Excel files which will automatically calculate the indicators when
the required data are entered. Separate forms are provided for Xpert MTB/RIF Testing Quality Indicators (Monthly
Report); Diagnostic Cascade Quality Indicators and QA System Process Indicators.
Training
Provides an overview of training materials from the Global Laboratory Initiative for Xpert users, advanced users, and
clinicians and nurses. Link for GLI modules: (http://www.stoptb.org/wg/gli/TrainingPackage_XPERT_MTB_RIF_Ultra.asp)
3. Competency assessment for GeneXpert users

Contains forms to perform and document competency assessments. Part A describes competency assessment for
GeneXpert users. Part B describes competency assessment for GeneXpert advanced users
4. Assessment Checklist for Testing Sites (ACTS) checklist and User’s Guide
Contains the Assessment Checklist for Testing Sites (ACTS) for conducting on-site supervisory visits. A user’s
manual is also provided.
Xpert MTB/RIF SOP

Contains an example of a standard operating procedure for conduction the Xpert MTB/RIF test.
https://www.finddx.org/implementation-resources/?level0=main-accordion-4&level1=secondary-left-accordion-1
5. Proficiency testing programme – guidelines and SOPs

Contains guidelines, forms and SOPs for producing proficiency testing panels in-country and conducting an Xpert
MTB/RIF Proficiency Testing program.
6. New lot testing SOP

Contains an SOP for quality control of new lots of Xpert cartridges.
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Xpert QA Guide 2019

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Practical Guide to

Standards and key activities for assuring quality 3

From standards and procedures to implementation 5

Part 1: National and supervisory levels 6

Element 2. Strategic planning 11

2.2. Prioritize interventions 13

2.3. Set the budget and time line 14

Element 3. Quality procedures and documentation 15

Element 4: Training, competency assessment and certification 17

4.2. Perform competency assessments 18

Element 5. Data connectivity and remote monitoring 20

Element 6. A safe and functional testing site 23

Element 7. Equipment and supplies 25

7.1. Equipment service and maintenance 25

7.2 Quality supplies 26

8. External quality assessment (EQA) 27

8.1. On-site supervision 27

8.2. Proficiency testing 28

9.2 Assign responsibilities for data collection, reporting and analysis 34

9.3 Collect, compile and analyse data 35

9.4 Evaluate progress and identify trends 36

2.1. Situational analysis 43

Element 3. Quality procedures and documentation 44

Element 4. Training, competency assessment and certification 46

4.2. Conduct and document competency assessments 47

Element 5. Diagnostics connectivity and remote monitoring 49

Element 6. A safe and functional testing site 51

6.1. Create and maintain a functional working environment 51

6.2. Create and maintain a safe working environment 52

Element 7. Equipment and supplies 55

7.1. Maintenance and calibration of the Genexpert instrument 55

7.2. Ensure adequate supplies & reagents 57

Element 8. Participate in an EQA programme 59

8.1. Participate in a system of supportive supervision and on-site evaluations 59

8.2. Test PT panels 60

Element 9. Monitor and analyse Xpert MTB/RIF quality indicators 61

9.1. Identify and implement quality indicator monitoring 61

9.2. Regularly review quality indicators and troubleshoot unexpected results

by identifying corrective actions 64

9.3. Report quality indicator data to the NTP/MOH 65

10.2. Test quality samples 67

10.3. Report accurate results 69

CDC U.S. Centers for Disease Control and Prevention

CQI Continuous quality improvement

DCS Dried culture spots

DNA Deoxyribonucleic acid

DST Drug susceptibility testing

DTS Dried tube spot

EQA External Quality Assurance / Assessment

GLI Global Laboratory Initiative

ISO International Organization for Standardization

M&E Monitoring and evaluation

MDR-TB Multidrug-resistant tuberculosis

MGIT Mycobacteria Growth Indicator Tube

MOH Ministry of Health

MTBC Mycobacterium tuberculosis complex

NHLS National Health Laboratory Service

NTP National TB Programme

NTRL National TB Reference Laboratory