Handbook on tuberculosis laboratory diagnostic methods in the European Union : updated 2018.
Date: 2018-09-11
Institutions: European Centre for Disease Prevention and Control
Subjects: disease prevention, harmonisation of standards, health control, health policy, infectious disease, public health, research body, research method, respiratory disease, user guide

       TECHNICAL REPORT   

Handbook on tuberculosis 
laboratory diagnostic methods 
in the European Union 

Updated 2018

www.ecdc.europa.eu

ECDC TECHNICAL REPORT 

Handbook on tuberculosis laboratory 
diagnostic methods in the European Union 
Updated 2018 

 
 
This report of the European Centre for Disease Prevention and Control (ECDC) was coordinated by Csaba Ködmön 
with support from Marieke J. van der Werf, Francis Drobniewski and Vladyslav Nikolayevskyy. 

This report was sent for consultation to the members of the ERLTB-Net network (see Appendix 1 for list of 
contributors). 

The first version of this ECDC technical report, previously published as ‘Mastering the basics of TB control: 
Development of a handbook on TB diagnostic methods’ (Stockholm 2011), concerned the development of the 
handbook that was included as an annex. This report was revised and renamed ‘Handbook on TB laboratory 
diagnostic methods in the European Union’ in 2016 and further revised and renamed ‘Handbook on tuberculosis 
laboratory diagnostic methods in the European Union – Updated 2018’ with changes to Chapters 6.7 and 10.4 in 
2018 as new scientific evidence became available. 

Suggested citation: European Centre for Disease Prevention and Control. Handbook on tuberculosis laboratory 
diagnostic methods in the European Union – Updated 2018. Stockholm: ECDC; 2018. 

Stockholm, August 2018 

ISBN 978-92-9498-264-3 
doi 10.2900/914169 
Catalogue number TQ-03-18-237-EN-N 

© European Centre for Disease Prevention and Control, 2018 

Reproduction is authorised, provided the source is acknowledged 

ii 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Contents 
Abbreviations ................................................................................................................................................ 5 
Background and introduction .......................................................................................................................... 6 
How this handbook relates to other work available in this field ........................................................................... 6 
What this document is/is not ........................................................................................................................... 6 
Intended use and users ................................................................................................................................... 7 
History of the handbook .................................................................................................................................. 7 
This edition .................................................................................................................................................... 7 
1 Biosafety in clinical laboratory diagnosis of tuberculosis ......................................................................... 7 
2 Quality assurance .............................................................................................................................. 7 
3 Latent TB infections ........................................................................................................................... 7 
4 Smear microscopy.............................................................................................................................. 7 
5 Culture for Mycobacterium tuberculosis complex ................................................................................... 7 
6 Identification of Mycobacterium tuberculosis and drug resistance in cultures and sputum using molecular 
assays ................................................................................................................................................. 8 
7 First- and second-line drug susceptibility testing for Mycobacterium tuberculosis complex ........................ 8 
8 Molecular typing of Mycobacterium tuberculosis complex isolates ........................................................... 8 
9 Use and validation of disinfectants for M. tuberculosis ........................................................................... 8 
10 Information for physicians: the laboratory diagnosis of tuberculosis – first steps .................................... 8 
Disclaimer ...................................................................................................................................................... 8 
1 Biosafety in the laboratory diagnosis of tuberculosis ....................................................................................... 9 
1.1 Background and principles ......................................................................................................................... 9 
1.2 The containment laboratory (biosafety level 3) .......................................................................................... 10 
1.2.1 General considerations ................................................................................................................ 10 
1.3 Laboratory facility .................................................................................................................................... 11 
1.4 Procedures ............................................................................................................................................. 12 
1.5 Personal protective equipment (PPE) ........................................................................................................ 12 
1.6 The human resource component .............................................................................................................. 13 
1.7 Specific laboratory tasks related to hazards ............................................................................................... 13 
References ................................................................................................................................................... 14 
Appendix ...................................................................................................................................................... 15 
2 Quality assurance ...................................................................................................................................... 17 
2.1 Background and principles ....................................................................................................................... 17 
2.2 Selection and implementation of tests ...................................................................................................... 18 
2.3 Validation ............................................................................................................................................... 19 
2.4 Control and trend monitoring by key indicators ......................................................................................... 19 
2.5 Physical and environmental conditions ...................................................................................................... 19 
2.6 Equipment .............................................................................................................................................. 20 
2.7 Management and staff ............................................................................................................................. 20 
2.8 Documentation and registration ............................................................................................................... 20 
2.9 Sampling guidance, review of requests and service to customers ............................................................... 20 
2.10 Subcontracting, services and supplies ..................................................................................................... 21 
2.11 Complaints, errors and corrective actions ................................................................................................ 21 
2.12 Improvements....................................................................................................................................... 21 
2.13 Reporting and releasing results .............................................................................................................. 21 
References ................................................................................................................................................... 21 
3. The diagnosis of latent TB infection ........................................................................................................... 22 
3.1 Background and principles ....................................................................................................................... 22 
3.1.1 Immune response to M. tuberculosis ............................................................................................ 22 
3.2 The tuberculin skin test (TST) .................................................................................................................. 23 
3.3 Interferon-γ release assays (IGRAs) ......................................................................................................... 23 
3.3.1 Introduction ............................................................................................................................... 23 
3.3.2 Current national guidelines and the clinical use of IGRAs ............................................................... 24 
3.3.3 Predictive value of IGRA for progression to active TB ..................................................................... 25 
3.3.4 IGRA performance and reproducibility .......................................................................................... 26 
3.3.5 Procedure 1: QuantiFERON-TB Gold and QuantiFERON-TB Gold PLUS ............................................. 26 
3.3.6 Procedure 2: T-SPOT procedure .................................................................................................. 30 
References ................................................................................................................................................... 34 
Appendix: Patient data sheet ......................................................................................................................... 36 
4. Smear microscopy .................................................................................................................................... 37 
4.1 Background and principles ....................................................................................................................... 37 
4.2 Procedure 1: Ziehl-Neelsen (ZN) .............................................................................................................. 37 
4.2.1 Ziehl-Neelsen (ZN) reagent preparation ........................................................................................ 37 
1 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

4.2.2 Storage of reagents .................................................................................................................... 39 
4.2.3 Quality control of freshly-prepared staining reagents ..................................................................... 39 
4.3 Procedure 2: Fluorochrome staining ......................................................................................................... 39 
4.3.1 Quality control of freshly-prepared staining reagents ..................................................................... 39 
4.3.2 Safety measures ........................................................................................................................ 40 
4.4 Sample collection .................................................................................................................................... 40 
4.4.1 Specimen handling ..................................................................................................................... 40 
4.4.2 Criteria of acceptability ............................................................................................................... 40 
4.5 Smear preparation .................................................................................................................................. 41 
4.6 Staining procedures ................................................................................................................................. 41 
4.6.1 Ziehl-Neelsen staining method ..................................................................................................... 41 
4.6.2 Fluorochrome staining method .................................................................................................... 42 
4.6.3 Automatic staining ...................................................................................................................... 42 
4.7 Microscopy.............................................................................................................................................. 42 
4.7.1 Maintenance .............................................................................................................................. 43 
4.7.2 Fluorescence microscopy............................................................................................................. 43 
4.7.3 Light-emitting diode (LED) microscopy ......................................................................................... 43 
4.8 Recording and reporting .......................................................................................................................... 43 
4.8.1 ZN smear examination ................................................................................................................ 44 
4.8.2 Auramine (fluorochrome) smear examination ................................................................................ 44 
4.9 Quality control ........................................................................................................................................ 45 
4.9.1 Quality control parameters .......................................................................................................... 45 
References ................................................................................................................................................... 45 
5. Culture tests for Mycobacterium tuberculosis complex ................................................................................. 47 
5.1 Background and principles ....................................................................................................................... 47 
5.2 Biohazards and biosafety in the TB laboratory ........................................................................................... 47 
5.2.1 Minimum WHO recommendations for TB culture/drug susceptibility testing facilities ......................... 48 
5.3 Specimen collection, storage and transport ............................................................................................... 49 
5.3.1 Sample collection ....................................................................................................................... 49 
5.3.2 Storage of specimens ................................................................................................................. 50 
5.3.3 Transportation of specimens ....................................................................................................... 50 
5.4 Homogenisation and decontamination of specimens .................................................................................. 50 
5.4.1 Digestion and decontamination of sputum samples ....................................................................... 51 
5.4.2 Digestion and decontamination of specimens other than sputum .................................................... 53 
5.5 Culture media: principles ......................................................................................................................... 54 
5.6 Solid media ............................................................................................................................................. 54 
5.6.1 Egg-based media ....................................................................................................................... 54 
5.6.2 Agar-based media ...................................................................................................................... 54 
5.6.3 Liquid media .............................................................................................................................. 55 
5.6.4 Quality control of media .............................................................................................................. 55 
5.7 Culture tube inoculation ........................................................................................................................... 55 
5.7.1 Solid media ................................................................................................................................ 55 
5.7.2 Liquid media .............................................................................................................................. 56 
5.8 Culture incubation ................................................................................................................................... 56 
5.9 Culture examination ................................................................................................................................ 56 
References ................................................................................................................................................... 58 
6. Identification of Mycobacterium tuberculosis and drug resistance in cultures and sputum using molecular assays 
and immunoassays ...................................................................................................................................... 59 
6.1 Background and principles ....................................................................................................................... 59 
6.2 Procedure 1: Chromatographic immunoassay for the qualitative detection of Mycobacterium tuberculosis 
complex from cultures ................................................................................................................................... 59 
6.2.1 Introduction ............................................................................................................................... 59 
6.2.2 Materials ................................................................................................................................... 59 
6.2.3 Methods .................................................................................................................................... 59 
6.2.4 Results/interpretation ................................................................................................................. 60 
6.2.5 Biosafety ................................................................................................................................... 60 

6.3 Procedure 2: Line probe assay for the identification of the genus Mycobacterium and 16 different 
mycobacterial species including M. tuberculosis complex from culture .............................................................. 60 
6.3.1 Introduction ............................................................................................................................... 61 
6.3.2 Materials ................................................................................................................................... 61 
6.3.3 Methods .................................................................................................................................... 61 
6.3.4 Results/interpretation ................................................................................................................. 61 
6.3.5 Biosafety ................................................................................................................................... 62 

6.4 Procedure 3: Line probe assay for the identification of the M. tuberculosis complex and the detection of 
rifampicin resistance in M. tuberculosis ........................................................................................................... 62 

2 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

6.4.1 Introduction ............................................................................................................................... 62 
6.4.2 Materials ................................................................................................................................... 62 
6.4.3 Methods .................................................................................................................................... 63 
6.4.4 Results/interpretation ................................................................................................................. 65 

6.5 Procedure 4: Line probe assay for identifying species from Mycobacterium genus and detecting potential 
multidrug and extensively multidrug-resistant tuberculosis (MDR- and XDR-TB) from cultures and smear-positive 
specimens .................................................................................................................................................... 67 
6.5.1 Introduction ............................................................................................................................... 67 
6.5.2 Materials ................................................................................................................................... 67 
6.5.3 Methods .................................................................................................................................... 68 
6.5.4 Results/interpretation ................................................................................................................. 70 
6.5.5 Examples of reporting for GenoType Mycobacterium MTBDRplus .................................................... 73 
6.5.6 Biosafety ................................................................................................................................... 73 
6.6 Procedure 5: Nucleic acid hybridisation test for the identification of M. tuberculosis complex ........................ 74 
6.6.1 Introduction ............................................................................................................................... 74 
6.6.2 Materials ................................................................................................................................... 74 
6.6.3 Methods .................................................................................................................................... 74 
6.6.4 Results/interpretation ................................................................................................................. 74 
6.6.5 Biosafety ................................................................................................................................... 74 

6.7 Procedure 6: Single-use sample-processing cartridge system with integrated multicolour real-time PCR 
capacity for detection, identification of M. tuberculosis complex bacteria and detection of rifampicin resistance .. 75 
6.7.1 Introduction ............................................................................................................................... 75 
6.7.2 Materials ................................................................................................................................... 75 
6.7.3 Methods .................................................................................................................................... 75 
6.7.4 Results/Interpretation ................................................................................................................. 75 
6.7.5 Biosafety ................................................................................................................................... 76 
References ................................................................................................................................................... 77 
7. First- and second-line drug susceptibility testing for Mycobacterium tuberculosis complex ............................... 78 
7.1 Background and principles ....................................................................................................................... 78 
7.2 Procedure 1: General method – DST by culture ......................................................................................... 78 
7.2.1 Introduction ............................................................................................................................... 78 
7.2.2 Materials ................................................................................................................................... 79 
7.2.3 Methods .................................................................................................................................... 79 
7.2.4 Safety ....................................................................................................................................... 79 
7.2.5 Report/interpretation .................................................................................................................. 79 
7.3 Procedure 2: Proportion method on Löwenstein-Jensen medium ................................................................ 80 
7.3.1 Introduction ............................................................................................................................... 80 
7.3.2 Definition ................................................................................................................................... 80 
7.3.3 Materials ................................................................................................................................... 80 
7.3.4 Methods .................................................................................................................................... 80 
7.3.5 Safety ....................................................................................................................................... 81 
7.3.6 Report interpretation .................................................................................................................. 81 
7.4 Procedure 3: Resistance ratio method ...................................................................................................... 82 
7.4.1 Introduction ............................................................................................................................... 82 
7.4.2 Materials ................................................................................................................................... 82 
7.4.3 Methods .................................................................................................................................... 82 
7.4.4 Safety ....................................................................................................................................... 83 
7.5 Procedure 4: Drug susceptibility testing in liquid media (µGIT 960) ............................................................ 84 
7.5.1 Introduction ............................................................................................................................... 84 
7.5.2 Materials ................................................................................................................................... 84 
7.5.3 Methods .................................................................................................................................... 84 
7.5.4 Safety ....................................................................................................................................... 84 
7.5.5 Report interpretation .................................................................................................................. 85 
7.6 Procedure 5: Other methods for first-line drug susceptibility testing............................................................ 85 
7.6.1 Absolute concentration method ................................................................................................... 85 
7.6.2 Nitrate reductase assay ............................................................................................................... 85 
7.6.3 Microscopically Observed Drug Susceptibility Assay (MODS) ........................................................... 86 
7.6.4 Colorimetric redox indicator (CRI) assay [31,32] ........................................................................... 86 
References ................................................................................................................................................... 87 
8. Molecular typing of Mycobacterium tuberculosis complex isolates ................................................................. 89 
8.1 Background and principles ....................................................................................................................... 89 
8.2 Procedure 1: Spoligotyping ...................................................................................................................... 89 
8.3 Procedure 2: MIRU-VNTR typing .............................................................................................................. 91 
8.4 Procedure 3: RFLP typing ........................................................................................................................ 92 
8.5 General considerations on routine genotyping methods ............................................................................. 92 
3 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

8.6 Procedure 4: whole genome sequencing ................................................................................................... 92 
8.7 Materials ................................................................................................................................................. 93 
8.8 Results/interpretation .............................................................................................................................. 94 
8.9 Quality control ........................................................................................................................................ 94 
8.10 Biosafety ............................................................................................................................................... 94 
References ................................................................................................................................................... 95 
9. Use and validation of disinfectants for Mycobacterium tuberculosis ............................................................... 98 
9.1 Liquid disinfection ................................................................................................................................... 98 
9.1.1 Suspension test: EN 14348:2005 ................................................................................................. 98 
9.1.2 Carrier Test: EN 14563:2008 ....................................................................................................... 99 
9.1.3 Choice of method to be used ..................................................................................................... 100 
9.2 Gaseous disinfection ............................................................................................................................... 100 
9.2.1 Vaporised hydrogen peroxide and hydrogen peroxide vapour ....................................................... 100 
9.2.2 Dry mist hydrogen peroxide ...................................................................................................... 101 
9.2.3 Plasma hydrogen peroxide ........................................................................................................ 101 
9.2.4 Use of gaseous disinfection in accident scenarios ........................................................................ 101 
References .................................................................................................................................................. 102 
10. Information for physicians: laboratory diagnosis of tuberculosis – first steps .............................................. 104 
10.1 Introduction ......................................................................................................................................... 104 
10.2 General considerations regarding the diagnosis of tuberculosis ................................................................ 104 
10.3 Specific considerations regarding diagnosis of tuberculosis ...................................................................... 105 
10.3.1 Pulmonary material ................................................................................................................. 105 
10.3.2 Pleural material ...................................................................................................................... 106 
10.3.3 Lymphadenitis material ........................................................................................................... 106 
10.3.4 Gastric juice ........................................................................................................................... 106 
10.3.5 Peritoneal fluid ....................................................................................................................... 106 
10.4 Information flow from microbiologist to physician and instructions regarding tuberculosis diagnosis .......... 106 
References .................................................................................................................................................. 107 
Annex 1. Network partners ......................................................................................................................... 109 
Figures 
Figure 1. Biohazard warning sign for laboratory doors ..................................................................................... 10 
Figure 2. Potential outcomes of human host infection by M. tuberculosis .......................................................... 23 
Figure 3. Microscope components .................................................................................................................. 42 
Figure 4. AFB smear microscopy of biological specimens ................................................................................. 44 
Figure 5. AFB smear microscopy of M. tuberculosis cultures ............................................................................. 44 
Figure 6. Minimal examination schedule for solid cultures ................................................................................ 57 
Figure 7. Examples of chromatographic immunoassays for qualitative detection of M. tuberculosis complex ......... 60 
Figure 8. Interpretation scheme for INNO-LiPA ............................................................................................... 62 
Figure 9. Interpretation of LiPA ..................................................................................................................... 66 
Figure 10. Interpretation sheet for GenoType Mycobacterium CM ..................................................................... 70 
Figure 11. Interpretation sheet for GenoType Mycobacterium AS ..................................................................... 71 
Figure 12. Interpretation sheet for GenoType Mycobacterium MTBC ................................................................. 71 
Figure 13. Interpretation sheet for GenoType Mycobacterium MTBDRplus ......................................................... 72 
Figure 14. Interpretation sheet for GenoType Mycobacterium MTBDRsl ............................................................ 72 
Tables 
Table 1 Examples of personal protective equipment..................................................................................................... 13 
Table 2. Overall scope of ISO 17025 and ISO 15189 .................................................................................................... 18 
Table 3. Central terms and abbreviations in quality assurance ...................................................................................... 18 
Table 4. List of national LTBI diagnosis guidelines........................................................................................................ 24 
Table 5. QuantiFERON-TB Gold results interpretation ................................................................................................... 29 
Table 6. QuantiFERON-TB Gold PLUS results interpretation .......................................................................................... 29 
Table 7. Materials provided by the manufacturer ......................................................................................................... 31 
Table 8. Equipment required for smear preparation and staining .................................................................................. 41 
Table 9. Reporting of microscopy smears .................................................................................................................... 43 
Table 10. Common causes of error in smear microscopy .............................................................................................. 45 
Table 11. Solvents and diluents ................................................................................................................................... 80 
Table 12. Calculation of modal MIC value .................................................................................................................... 82 
Table 13. Examples of MIC interpretation .................................................................................................................... 83 
Table 14. Critical concentrations of the most important first- and second-/third-line drugs ............................................ 84 
Table 15. Differences between the two major gaseous hydrogen peroxide technologies, Steris VHP and Bioquell HPV . 101 

4 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Abbreviations 

AFB 
BCG 
BD 
BSC 
BSL 
CFU 
CSF 
CRI 
CXR 
DNA 
DST 
EEA 
ENP 
EPTB 
ERLN-TB 
ERLTB-Net 
EQA 
EU 
HEPA filter 
HPF 
IATA 
IFN-γ 
INSTAND e.V. 
IGRA 
IQA 
ISO 
LED 
LJ medium 
LTBI 
µGIT 
MIC 
MIRU 
MODS 
MTBC 
NAAT 
NRA 
NRL 
NTM 
PBMC 
PCR 
PPD 
PPE 
PPV 
QA 
QC 
RFLP 
RNI 
SDS  
SNP 
SOP 
TB 
TST 
UKAS 
UK NEQAS 
VNTR 
ZN 

Acid-fast bacilli 
Bacillus Calmette-Guérin 
Becton and Dickinson 
Biological safety cabinet 
Biosafety level 
Colony forming units 
Cerebral spinal fluid 
Colorimetric redox indicator 
Chest X-ray 
Deoxyribonucleic acid 
Drug susceptibility testing 
European Economic Area 
European Neighbourhood Policy 
Extrapulmonary tuberculosis 
European Reference Laboratory Network for Tuberculosis (2010–2014) 
European Reference Laboratory Network for Tuberculosis (from 2014) 
External quality assessment 
European Union 
High-efficiency particulate air filter 
High-power field 
International Air Transport Association 
Interferon-gamma 
Society for promoting quality assurance in medical laboratories 
Interferon-gamma release assay 
Internal quality assessment 
International Organization for Standardization 
Light-emitting diode 
Löwenstein-Jensen medium 
Latent TB infection 
Mycobacteria growth indicator tube 
Minimum inhibitory concentration 
Mycobacterial interspersed repetitive units 
Microscopically observed drug susceptibility 
Mycobacterium tuberculosis complex 
Nucleic-acid amplification test 
Nitrate reductase assay 
National reference laboratory 
Non-tuberculous mycobacteria 
Peripheral blood mononuclear cells 
Polymerase chain reaction 
Purified protein derivative 
Personal protective equipment 
Positive predictive value 
Quality assurance 
Quality control 
Restriction fragment length polymorphism 
Reactive nitrogen intermediates 
Sodium dodecyl sulfate 
Single nucleotide polymorphism 
Standard operating procedures 
Tuberculosis 
Tuberculin skin test 
United Kingdom Accreditation Service 
UKAS accredited proficiency testing provider No. 4715 
Variable number tandem repeat 
Ziehl-Neelsen (staining method) 

5 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Background and introduction 

Francis Drobniewski 

Tuberculosis (TB) is a major cause of morbidity and mortality in Europe. High-quality laboratory diagnosis of TB is 
the basis for both individual patient treatment and surveillance. 

In 2007, a survey of existing mycobacterial laboratory services and quality control practices throughout the EU 
confirmed the key role of national reference laboratories (NRL) for TB and their services. The main conclusion of 
the survey was that a network of reference laboratories for tuberculosis could contribute to improving the 
performance of mycobacterial laboratories in Europe. 

Based on these results, the European Reference Laboratory Network for Tuberculosis (ERLN-TB) was launched in 
January 2010, with the aim of strengthening TB diagnostics in the European Union. ERLN-TB was funded and 
coordinated by ECDC. One or two officially nominated reference laboratories from each Member State joined the 
network, along with those in EEA countries and EU candidate countries. 

Following the success of the ERLN-TB network, in 2014 ECDC commissioned a renewal of the network (now called 
European Reference Laboratory TB-Network [ERLTB-Net]) involving the same centres but anticipating the 
participation of institutions from the EU enlargement countries in the longer-term. 

The three main goals of the new network are: to support the harmonisation of laboratory methods within the 
EU/EEA; develop External Quality Assurance (EQA) schemes and provide training activities within the network to 
ensure EU-wide capacity-building for TB diagnostics. One of the main activities conducted by the network was the 
development of a handbook of key diagnostic methods for tuberculosis which was first published in 2011. This 
document represents the latest version of the handbook. 

The aim of this handbook is to provide network members and other laboratories involved in the diagnosis of 
tuberculosis, with an agreed list of key diagnostic methods and their protocols in various areas of TB diagnosis, 
ranging from microbiological diagnosis of active TB to the diagnosis of latent TB infection (LTBI). This handbook 
offers a single source of reference by compiling all methods, with a strong focus on standard (reference) and 
evidence-based methods. 

The handbook will also contribute to the improvement of disease surveillance data for Europe: data sent to ECDC’s 
TESSy (The European Surveillance System) and other surveillance systems should be robust and backed by quality 
laboratory diagnostics. 

The handbook addresses the changing technological landscape that has emerged over the last decade, particularly 
with regard to non-microbiological assays and platforms. Much of this technology has led to a major shift in TB 
diagnostic activities with the development of multiple, large and well-equipped diagnostic centres with similar 
capacity and skills to national reference laboratories (e.g. rapid molecular diagnostic tests). Conversely, other 
molecular diagnostic developments have moved us away from ‘big laboratory’ approaches and closer to ‘point-of-
care’ devices. The two approaches are not mutually exclusive and both bring advanced diagnostics closer to the 
patient. The handbook is designed to meet the needs of both centralised and decentralised service delivery models 
and recognises that the role of national reference laboratories will change significantly over the next few years. 

How this handbook relates to other work available in this 
field 

This handbook presents a compilation of methods currently applied in EU/EEA Member States. It describes 
common work carried out and endorsed by European laboratory experts. It also features methods and procedures 
developed or refined by ERLTB-Net network partners. 

What this document is/is not 

This document is a handbook of agreed methods in the field of TB diagnostics for laboratories serving reference 
functions in Europe. It provides a comprehensive compilation of key methods for the diagnosis of TB. Relevant 
stakeholders are encouraged to use this compilation as a basis for the validation, development, updating and 
dissemination of information. 

The current document does not contain any formal recommendations for implementation of specific methods in 
EU/EEA Member States. Recommendations and protocols contained within the handbook are not mandatory for 
EU/EEA laboratories. 

6 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Intended use and users 

The report, which provides both basic- and reference-level methods for the diagnosis of TB, is intended for use by 
laboratory experts. It will also be of interest to public health professionals in the field of global TB control, 
particularly those involved in European initiatives to foster progress towards elimination of TB. 

History of the handbook 

The first annual meeting of the ERLN-TB was held in Stockholm in 2010. During this meeting, the network partners 
came to a consensus agreement about the relevant topics to be included in a handbook on (reference) laboratory 
methods for the diagnosis of TB. The approach was to include several standardised and reliable methods, rather 
than to focus on one single method. A dedicated writing committee was formed to compile the first draft of these 
methods, using a handbook format. Each chapter includes descriptions of standardised diagnostic methods and 
highlights key considerations regarding biosafety and quality assurance. 

The first edition was published in 2011. The handbook was extensively revised during 2014–2015 following the 
formation of the new ERLTB-Net network and in light of decisions made during its first annual meeting in 
September 2014. A draft of the handbook was sent out to all ERLTB-Net network partners for review and 
endorsement in February 2015. An approved version was submitted to ECDC in March 2015. 

This edition 

This handbook represents the second edition of a publication on the most reliable TB diagnostic methods, 
endorsed by the members of the ERLTB-Net. This publication is a compilation of protocols for the laboratory 
diagnosis of TB, designed for laboratory experts and public health professionals. It was compiled to contribute to 
the harmonisation of methods in the field of TB diagnosis in the EU/EEA, EU enlargement countries and European 
Neighbourhood Policy (ENP) partner countries, with the goal of ensuring comparability of TB diagnoses in Europe, 
and provision of the best care possible for TB patients, based on a quality-assured diagnosis. This publication can 
also support laboratories in establishing a safe working environment for staff by minimising the risk of exposure to 
M. tuberculosis. The second edition of the ERLTB-Net handbook consists of ten chapters, each with a list of 
relevant references. Below is a summary of each chapter. 

1 Biosafety in clinical laboratory diagnosis of tuberculosis 

M. tuberculosis can cause laboratory-acquired infections. In order to ensure effective infection control, it is crucial 
that a comprehensive and strict biosafety policy is developed and followed. Such a policy includes standardised 
rules and regulations for containment, personal protective equipment (PPE), standard operating procedures (SOP) 
for different laboratory tasks and a transparent structure for regulating safe working conditions in diagnostic TB 
laboratories. 

2 Quality assurance 

National tuberculosis programmes are supported by laboratories that provide reliable and quality-assured results. 
The chapter provides a comprehensive overview of existing International Organization for Standardization (ISO) 
standards relevant for the laboratory diagnosis of TB and describes internal and external quality assurance 
procedures. 

3 Latent TB infections 

Currently, two types of tests are used for the diagnosis of latent TB infections (LTBI): tuberculin skin tests (TSTs) 
and Interferon-γ release assays (IGRAs). The chapter describes in detail the two commercially available IGRAs for 
the detection of latent TB infection and provides support for interpreting and reporting test results. 

4 Smear microscopy 

Two types of staining are most commonly used for the detection of mycobacteria: carbol-fuchsin staining (Ziehl-
Neelsen, Kinyoun) and fluorochrome staining (auramine, auramine-rhodamine). The chapter describes the 
preparation of the required reagents and the sputum smear samples, as well as the staining procedures and the 
system foe reporting results. 

5 Culture for Mycobacterium tuberculosis complex 

The use of cultures improves the sensitivity and specificity of TB tests, particularly at the early stages of the 
disease, in cases of extrapulmonary tuberculosis (EPTB) and in the event of treatment failure. The chapter provides 
an overview of key principles for sampling and transporting clinical specimens and processing sputum and other 

7 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

specimens before inoculation to solid and liquid culture media, culture incubation and examination. The issue of 
contamination is addressed, along with the measures necessary to prevent laboratory-acquired TB infections. 

6 Identification of Mycobacterium tuberculosis and drug resistance in 
cultures and sputum using molecular assays 

Growth of mycobacteria in culture media can take up to eight weeks as M. tuberculosis and many other 
mycobacteria grow very slowly. This can lead to a delay in the treatment of patients. Molecular assays can speed 
up mycobacterium identification and drug susceptibility testing, and thus lead to faster and more specific 
treatment. The chapter describes methods for the identification of mycobacteria and drug susceptibility from 
culture and clinical specimens and gives suggestions for the interpretation and reporting of results. 

7 First- and second-line drug susceptibility testing for Mycobacterium 
tuberculosis complex 

The main objectives of drug susceptibility testing are to improve individual treatment management of tuberculosis 
cases and drug-resistance surveillance at the level of a hospital, city, region, or country. The chapter describes 
three different methods for drug susceptibility testing of first- and second-line drugs on solid and liquid media. 

8 Molecular typing of Mycobacterium tuberculosis complex isolates 

Various DNA fingerprinting methods are currently available that serve different purposes and have variable 
characteristics for specific applications. This chapter describes the three most important and widely applied 
methods (spoligotyping, variable number tandem repeat [VNTR] typing, IS6110 restriction fragment length 
polymorphism [RFLP] typing) and their application. 

9 Use and validation of disinfectants for M. tuberculosis 

In Containment Level 3 laboratories handling M. tuberculosis, liquid and gaseous methods are currently in use for 
disinfection and decontamination. The efficacy of any new disinfectants is analysed using a set of standard 
validation methods. 

10 Information for physicians: the laboratory diagnosis of 
tuberculosis – first steps 

The process of collecting material for the diagnosis of mycobacteria requires great care, as each step can influence 
the diagnosis. This chapter provides general information on the diagnosis of TB and gives specific instructions for 
the collection and treatment of clinical samples. 

Disclaimer 

Some protocols included in the handbook list specific commercial products and assays. Such instances do not 
constitute endorsement of relevant products by the ECDC. 

8 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

1 Biosafety in the laboratory diagnosis of 
tuberculosis 

Maryse Fauville-Dufaux, Vincent Jarlier, Dick van Soolingen, Sven Hoffner 

Revised by Dick van Soolingen, Dimitrios Papaventsis, Melles Haile and Sven Hoffner (2014) 

Note: This chapter largely consists of a summary of principles and procedures previously published by the World 
Health Organisation [1]. It focuses on aspects relevant to the infrastructure of European diagnostic laboratories for 
TB. For a more comprehensive view, please refer to the publications listed at the end of this chapter. 

1.1 Background and principles 

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is classified as a risk group 3 agent, which 
calls for a Biosafety Level 3 laboratory (BSL3) for culture, drug susceptibility testing and other laboratory 
examinations. Access to a safety laboratory should be restricted to staff members and accredited visitors [1]. This 
chapter describes the most important features of the facility, the procedures, and the personal protective 
equipment required to ensure biosafety. 

It is well documented that M. tuberculosis can cause laboratory-acquired infections and the risk of TB among 
healthcare workers is consistently higher than the risk in the general population [2]. M. tuberculosis even features 
in the top-ten list of hazardous agents for laboratory staff, however the source of the TB infection can only be 
traced to a specific laboratory accident in a minority of cases [3-5]. The most important route for laboratory-
acquired infections is aerosols. Thus, infection control efforts need to focus on limiting the generation of aerosols 
during laboratory work, for example through safe centrifugation and pipetting. The potential risk of infection 
depends on the type of techniques used and the way they are executed. For example, needle stick injuries are rare 
as in most laboratories the BD Bactec 460 system has been replaced by the µGIT 960 system, which does not use 
needles for the inoculation of test vials. Moreover, improvements in quality as a result of regular validation and 
proper use of biosafety cabinets have significantly enhanced infection control. 

For effective infection control it is crucial that a comprehensive and strict biosafety policy is developed, accepted 
and followed by the laboratory staff. The policy should include standardised rules and regulations for containment; 
personal protective equipment (PPE); a set of standard operating procedures (SOPs) for all the different laboratory 
tasks and transparent and clearly defined levels of responsibility for establishing and maintaining safe working 
conditions in the diagnostic TB laboratory [1,3,6,7]. In addition to the necessary training, there should be regular 
interaction between the responsible manager and the laboratory staff on interpretation of the rules and potential 
biosafety hazard to verify commitment and optimise follow-up of the implemented procedures. 

In the 2012 version of the WHO manual on biosafety in TB laboratories [8] more emphasis was placed on risk 
assessment. The risk of laboratory infections due to M. tuberculosis is related to the concentration of bacteria and 
the possible induction of aerosols. The handling of clinical specimens such as sputum (e.g. for smear examination 
and culture inoculation) poses a lower biohazard than working with positive cultures of the bacteria (e.g. for drug 
susceptibility testing). Therefore, sputum smear microscopy, treatment of specimens before culture, and DNA 
extraction from clinical specimens for molecular techniques (DNA identification, detection of gene mutations related 
to drug resistance or possible genotyping) may be carried out in a BSL2 laboratory setting. Nevertheless, the use of 
a well-functioning and regularly-serviced biosafety cabinet remains important when working with suspected M. 
tuberculosis material. Techniques performed on Mycobacterium cultures, such as the extraction of DNA from 
positive cultures and phenotypic drug susceptibility testing, require a higher level of biosafety and the use of a 
BSL3 containment laboratory. Molecular techniques involving previously extracted DNA do not require a biosafety 
level standard [1,3,6]. 

Before initiating a new test, task or method in a laboratory, a risk assessment is obligatory. This will identify 
possible risks and allow for proper infection control measurements. In 2008, the European Committee for 
Standardization (CEN) published the CWA 15793 Laboratory Biorisk Management Standard, which is based on a 
management systems approach [9]. Both CWA 15793:2008 and its latest version CWA 15793:2011 are laboratory 
biorisk management system agreements, establishing the requirements necessary to control risks associated with 
the handling or storage and disposal of biological agents and toxins in laboratories and facilities [10,11]. These 
standards use risk classifications described in the WHO Laboratory biosafety manual and formed the basis for 
development of the minimum requirements for TB diagnostic laboratories, described in the 2012 edition of the 
WHO Tuberculosis Laboratory biosafety manual [8]. 

9 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Appropriate infection control measures are necessary to enable laboratory staff to work safely with potentially 
infectious microorganisms. These measures are based on the following four main components: 

 
 
 
 

administration (management) 
environment (engineering) 
personal protective equipment (PPE) 
technical expertise and training (good microbiological practices). 

If correctly implemented, each of these components will help lower the risk of exposing laboratory personnel to the 
pathogen. 

A scheme for biosafety training and registration of laboratory staff experience levels is a useful tool for reducing 
the risk of laboratory infections. New staff members and regular laboratory staff should periodically undergo 
medical examination to document any laboratory-acquired infections and to offer preventive therapy or full 
treatment according to national guidelines. This will also make it possible to improve procedures that may have 
contributed to the LAI and will ensure that management and staff continue to focus on biosafety. 

The biosafety policy and guidelines should be based on national and international regulations, as well the specific 
local risk assessment for each stage of clinical diagnostic work. Since international recommendations might change 
over time and are often not very detailed, it is of great importance to always base new biosafety instructions on 
the most recent sources and to implement a regular update of the biosafety policy [1,6]. 

This chapter is based on available biosafety recommendations at the time of writing (September 2013), and should 
not be seen as a replacement of other international recommendations. The recently released WHO TB Laboratory 
biosafety manual [8] differs in its approach by putting less emphasis on each and every detail of a fully established 
BSL3 laboratory, and emphasising the importance of risk assessment in relation to the work conducted by TB 
laboratories at different levels. ECDC has also worked with an expert group of biosafety professionals [12], on a 
risk-based approach analysing work practices in TB laboratories in Europe and in 2013 it produced important 
recommendations for the ERLN-TB [12,13]. This chapter reflects the views of the authors and does not imply an 
endorsement by ECDC. 

1.2 The containment laboratory (biosafety level 3) 

1.2.1 General considerations 

The international biohazard warning symbol and other relevant signs displayed on laboratory access doors must 
identify the biosafety level and the name of the laboratory supervisor controlling access (Figure 1). Signs should 
also indicate the conditions for access, for example use of respirators and immunisation requirements. The best 
way to control access and also enable a retrospective check-up of all staff that entered the BSL3 laboratory at a 
particular point in time, is to use an electronic pass system. Any maintenance or technical personnel should always 
be accompanied by an authorised staff member and only be allowed access when the laboratory is considered 
relatively safe and if they are wearing personal protective equipment and the appropriate gown and shoes [1]. 

Figure 1. Biohazard warning sign for laboratory doors 

Source: World Health Organization. Laboratory biosafety manual, 3rd edition. Geneva; 2004 [1] 

10 

 
 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Inside the laboratory, protective clothing and shoes are used in accordance with local regulations. It is 
recommended that non-permeable/waterproof laboratory coats be used, either with a solid front or a wrap-around 
cut. Where appropriate, shoe covers (overshoes) or dedicated shoes should be worn. Front-buttoned standard 
laboratory coats are unsuitable, as are sleeves that do not fully cover the forearms. When working in the biosafety 
cabinet, the cuffs of the gown should be covered by disposable gloves to prevent contamination of the sleeves. 
Laboratory protective clothing should never be worn outside the laboratory and should be decontaminated before 
being laundered. Potentially infectious material should always be handled in a biological safety cabinet 
(corresponding to specific standards – e.g. BS EN 12469:2000 or NSF/ANSI 49-2008). Respiratory protective 
equipment is necessary for some laboratory procedures [1]. 

1.3 Laboratory facility 

There are many technical aspects to be considered before a BSL2 or BSL3 facility is constructed. Planning includes 
choice of equipment, ventilation system, technical maintenance and waste management, including the placing of 
the autoclave. All details of the construction should be documented and strictly follow the relevant rules and 
regulations at national level. If no national rules have been established, application of international rules is advised. 
The choice between BSL2 and BSL3 or a combination of BSL2 and BSL3 zones in the same facility is based on 
European and national regulations and is dependent on a risk assessment of the type of work to be carried out in 
the facility. 

The laboratory should be separated from areas that offer unrestricted entrance to the building. If the laboratory 
cannot be located in a separate, dedicated building, separation may be achieved by placing the laboratory at the 
blind end of a corridor, or by constructing a partition and a door or only allowing access through an anteroom. The 
anteroom should have clearly demarcated zones, with facilities for separating clean and dirty clothing and a 
shower. The anteroom doors should be self-closing and should open/close in the right direction to facilitate 
differences in pressure. The doors should also be interlocked, so that only one door can be open at a time. Ideally, 
there should be an electronic delay system that only allows the opening of one of the doors when the pressure in 
the anteroom has been restored. Depending on its size and shape the laboratory should have a break-through 
panel or emergency exit for use in case of emergencies [1,3]. 

As a rule, the following issues should be taken into consideration [1,3]: 

 
 

 

 

 
 
 
 
 

 
 

 

 

 

 

 

 

Ample space should be provided around the equipment for cleaning and maintenance. 
Walls, ceilings and floors should be non-absorbent, easy-to-clean, impermeable to liquids and resistant to 
the chemicals and disinfectants normally used in the laboratory. Floors should be slip resistant. 
Openings through these surfaces (e.g. for service pipes) should be sealed to prevent leakage and facilitate 
decontamination of the room/s using gas. 
Bench tops should be impervious to water and resistant to disinfectants, acids, bases, organic solvents and 
moderate heat. 
Lighting should be adequate for all activities. Undesirable reflections and glare should be avoided. 
Laboratory furniture should be sturdy. 
Open spaces between and under benches, cabinets and equipment should be accessible for cleaning. 
Windows should be sealed and break-resistant. 
Storage space must be adequate to hold supplies for immediate use and thus prevent clutter on bench tops 
and in aisles. Additional long-term storage space, conveniently located outside the laboratory working 
areas, should also be provided for storage of samples, cultures, records and for designated laboratory waste 
prior to autoclaving. 
A hand-washing station with hands-free controls should be provided near the exit door. 
To contain unintended release of aerosols, a controlled ventilation system should continuously maintain the 
negative pressure. A visual monitoring device should be placed at the entrance and in the inside of the 
laboratory to enable the pressure to be checked. 
There should be an alarm to warn personnel when pressure is out of range without causing panic or 
undesirable reactions. 
The building ventilation system should be installed in such a way that air from the containment laboratory 
can never be recirculated to other sections of the building. 
Air from the BSL3 laboratory should be filtered by HEPA filters. When air extracted from the laboratory is 
discharged to the outside of the building, it must be dispersed away from occupied buildings and air 
intakes. A heating, ventilation and air-conditioning control system may be installed to prevent positive 
pressurisation of the laboratory. 
The HEPA filters must be installed in a manner that permits gaseous decontamination and testing. The 
exhausted air from biological safety cabinets, which will have been passed through HEPA filters, should be 
discharged so that it does not interfere with the air balance in the laboratory. 
Biological safety cabinets should be situated away from walking areas and cross-currents from doors and 
ventilation systems. 
There should be a programme in place for the regular testing and validation of biological safety cabinets. 

11 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 

 

 

 

 
 

An autoclave for the decontamination of contaminated waste material should be available in the 
containment laboratory, ideally in the wall. In this way containers with contaminated waste can be uploaded 
in the BSL3 laboratory and, after the autoclave procedure, safely removed in a clean zone outside of the 
laboratory. In accordance with local regulations in some countries, the autoclave may be connected to the 
laboratory, located in the same building. In this case infectious waste must be transported in sealed, 
unbreakable and leak-proof containers in accordance with national or international regulations, as 
appropriate. These containers should preferably have vents that open when the containers are heated, so 
the steam can exit the containers. 
Waste water coming from the sinks installed in BSL3 should be decontaminated in kill tanks. Otherwise, if 
decontamination facilities are not available, sinks should not be installed. 
Safety systems should be implemented to handle the risks of fire and electrical emergencies. An emergency 
shower and an eyewash facility should also be installed. 
Suitably equipped and readily accessible first-aid areas or rooms should be available near the BSL3 
laboratory. The personnel of a BSL3 laboratory should ideally have received first-aid training. 
A mechanical ventilation system should provide an inward flow of air without recirculation.  
There should be a reliable and adequate electricity supply and emergency lighting to permit safe exit. A 
back-up system is highly important (e.g. a stand-by generator and a UPS to support alarm systems and 
other essential equipment such as biological safety cabinets, freezers, etc.) 

General requirements to the BSL3 facility are summarised in the appendix to Chapter 1. 

1.4 Procedures 

Based on local risk assessments, a set of detailed standard operating procedures should be developed and 
implemented for the safe performance of all tasks carried out in the facility. As a rule, the following procedures 
should be adhered to [1,6,8]: 

 
 

 

 

 

 

 

 

Pipetting by mouth must be strictly forbidden. 
All technical procedures should be performed so as to minimise the formation of aerosols and droplets. The 
use of any sharp objects, such as hypodermic needles and syringes, should be avoided. 
All spills, accidents and overt or potential exposures to infectious materials must be reported to the 
laboratory supervisor. A written record of such accidents and incidents (including precautions that will be 
taken to avoid similar accidents in the future) should be maintained. 
There should be a procedure in place for emergency action to be undertaken after any unintended release 
of bacteria and possible exposure of staff, including a medical surveillance programme. 
A written procedure must be developed for the cleaning-up of all spills. All staff members must be trained 
regularly and should have a good knowledge of, and a high level of compliance with all biosafety 
instructions.  
A spill emergency kit should be available with all required material to undertake immediate action in the 
event of a spill. 
All staff should always have an appropriate mask in their gown to put on if there is an unintended release of 
bacteria. 
Potentially contaminated liquids must be decontaminated (autoclaved) before being discharged into the 
public sewer system. 

1.5 Personal protective equipment (PPE) 

The use of Personal Protective Equipment (PPE) should be regulated in local standard operating procedures and be 
based on a local risk assessment as well as national and international regulations. It is crucial that the agreed 
choice of PPE is accepted, respected and followed by all staff members and visitors [1,6,8]. 

Table 1, adapted from the WHO Laboratory Biosafety Manual [1], lists examples of personal protection items for 
laboratory workers [1,8]. 

12 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Table 1. Examples of personal protective equipment 

Equipment 

Hazard corrected 

Safety features 

Contamination of clothing 

Back opening. Cover normal clothes 

Laboratory coats, gowns, 
coveralls 
Plastic aprons 
Footwear 

Contamination of clothing 
Impact and splash 

Goggles 

Impact and splash 

Safety spectacles 

Impact 

Face shields 

Impact and splash 

Respirators 

Inhalation of aerosols 

Gloves 

Direct contact with 
microorganisms, cuts 

Waterproof 
Closed-toe 
Impact-resistant lenses (must be optically correct 
or worn over corrective glasses). Side shields 
Impact-resistant lenses (must be optically correct). 
Side shields 
Shield entire face. Easily removable in case of 
accident 
Designs available include single-use disposable, 
full-face or half-face air purifying, full-face or 
hooded powered air purifying (PAPR) and 
supplied air respirators 
Disposable, microbiologically approved latex, vinyl 
or nitrile; hand protection; mesh 

Please refer to Chapter 5 for further details on laboratory safety levels and conditions when working with 
mycobacterial cultures. 

1.6 The human resource component 

Even the technically most advanced biosafety facility will fail if the laboratory staff neglects the biosafety rules. It is 
recommended that experienced technical staff members remain involved throughout the planning and 
implementation of the biosafety programme and establishment of the laboratory [1,6]. 

A well-designed training programme for biosafety, offered on an annual basis to all staff members, will raise the 
level of knowledge on the laboratory infection control plan. New staff members, as well as students and/or visiting 
researchers should be informed of all relevant rules and recommendations before being allowed to work in the 
laboratory. When they begin working in the laboratory they should never work independently, but be guided by 
experienced staff. It is recommended that the person responsible (often the laboratory supervisor) should inform 
them of all rules and regulations governing the laboratory and test their knowledge before they begin the actual 
laboratory work with the pathogen. Procedures governing medical emergencies and accidental exposure to 
infectious material should be in place. All reported events should be investigated and discussed extensively. This 
should be done in an atmosphere of cooperation to avoid staff members covering up details or becoming less 
inclined to report incidences/accidents in the future. A written suggestion for improvement should be prepared, 
describing in detail the preventive measures to be taken. 

It is the responsibility of all staff members to achieve and maintain a safe working environment. Good biosafety 
laboratory practices should be known and embraced by all staff members, both to prevent accidents and to avoid a 
staff member claiming ignorance of the safety guidelines after an accident. There should be a clear consensus on 
the interpretation and application of the rules; otherwise they should be adapted so that all staff adhere to the 
local and international regulations. 

1.7 Specific laboratory tasks related to hazards 

As mentioned above, the risk of laboratory infections due to M. tuberculosis is related to the concentration of 
bacteria and the possible creation of infectious aerosols. 

Biosafety measures must always be based on risk assessment [1,6,8]. Here are some examples: 

 

 

 

Handling of containers with clinical specimens. Even if it is unlikely to generate aerosols, exposure to 
the tubercle bacilli is possible. The outsides of containers used for the collection of clinical specimens are 
frequently contaminated by M. tuberculosis or other airborne pathogens. Specimen containers should 
therefore be handled carefully and only be opened in a biological safety cabinet. 

Centrifugation. Fluid may spill from centrifuge tubes or tubes may break, releasing aerosols. Only closed 
biosafety cups with appropriate and safe centrifugation tubes should be used. Centrifuge safety cups should 
therefore only be loaded/unloaded in the biological safety cabinet. 
Pipetting. Pipettes and Pasteur pipettes in particular are likely to generate bubbles that burst and form 
aerosols. Pipetting should therefore always be performed in biological safety cabinets and by using 
disposable pipettes. Pipetting by mouth is strictly forbidden. 

13 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 

 

 

 

 

 

Mechanical homogenising (vortexing, grinding, blending). Appropriate procedures to avoid the 
induction of aerosols should be in place. Mechanical homogenisation should always be carried out in a 
biological safety cabinet and even then it still creates a risk. 
Sonication, heating or boiling of samples (e.g. for the extraction of nucleic acids). Appropriate 
procedures should be applied to avoid splashing and the creation of aerosols. 
Use of bacteriological loops. Loops charged with infectious material should not be directly heated in the 
flame of a Bunsen burner due to the risk of splashing and the creation of aerosols. Bunsen burners must 
not be used in a biosafety cabinet because this disturbs the flow of air. The use of disposable plastic loops 
is highly recommended. 

Animal studies. Major risks to staff are self-inoculation with material meant to infect the animals and 
exposure to aerosols from diseased animals. The litter of infected animals can also be contaminated and 
thus become a potential source of infection. 
Transport and shipping of M. tuberculosis strains. There are strict rules that must be followed when 
transporting suspected clinical samples, in particular cultured M. tuberculosis. These transport rules depend 
on arrangements within a country, between countries or with regard to air transportation. It is the 
responsibility of the shipping laboratory to identify the relevant regulations and follow them strictly. The use 
of dedicated couriers specialised in transport of BSL3 material and familiar with all regulations is highly 
recommended. All requested procedures must be fulfilled by the sender laboratory to ensure correct 
packing. 

Storing collections of M. tuberculosis isolates and reference strains. There should be local 
procedures with regard to biosafety for the storage of bacteria and clinical specimens containing bacteria. 
All freezers, fridges and other storage cabinets should be properly labelled, with the person in charge clearly 
marked. Access to the freezers should be limited to specific laboratory staff. The stock of BSL3 cultures 
should be registered in order to identify any illegal removal or unexplained disappearance. 

References 

World Health Organization. Laboratory biosafety manual. 3rd edition.Geneva: WHO;2004. Available from: 
http://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf. 

Baussano I, Williams B, Pivetta E, Bugiani M, Scano F. Tuberculosis among healthcare workers. Emerg Infect 
Dis 2011, 17:488–494. 

Fleming DO, Hunt DL, Editors. Biological safety: principles and practices., 4th ed. Washington:AS M Press; 
2006. 

Collins CH, Kennedy DA. Laboratory-acquired infections: history, incidence, causes and prevention. 4th 
ed.Oxford: Butterworth-Heinemann; 1999. 

Sewell DL. Laboratory-acquired infections: Are microbiologists at risk? Clin Microbiol Newsl. 2006;1:1-6. 

US Department of Health and Human Services, Public Health Service, Centers for Disease Control and 
Prevention, National Institutes of Health. Biosafety in microbiological and biomedical laboratories. 5th ed. 
Washington: CDC/NIH; 2009. Available from: http://www.cdc.gov/biosafety/publications/bmbl5/BMBL.pdf. 

Miller JM, Astles R, Baszler T, Chapin K, Carey R, Garcia L, et. al. Guidelines for safe work practices in 
human and animal medical diagnostic laboratories.Recommendations of a CDC-convened, Biosafety Blue 
Ribbon Panel.MMWR Surveill Summ.2012 Jan 6;61 Suppl:1-102. 

World Health Organization. Tuberculosis laboratory biosafety manual. Geneva: WHO; 2012.. Available from: 
http://apps.who.int/iris/bitstream/10665/77949/1/9789241504638_eng.pdf. 

CEN. Laboratory Biorisk Management Standard CWA 15793:2008. Brussels; 2011. Available from: 
ftp://ftp.cenorm.be/PUBLIC/CWAs/wokrshop31/CWA15793.pdf. 

CEN. Laboratory Biorisk Management Standard CWA 15793: 2011.Brussels; 2011. Available from: 
ftp://ftp.cenorm.be/CEN/Sectors/TCandWorkshops/Workshops/CWA15793_September2011.pdf. 

CEN. Laboratory biorisk management Standard CWA 16393- Guidelines for the implementation of CWA 
15793:2008. Brussels; 2012. Available from: 
ftp://ftp.cen.eu/CEN/Sectors/list/ICT/Workshops/CWA%2016393.pdf. 

ECDC: Biorisk Initiative for Capacity Building and Knowledge Base Development (BRICK): Available from: 
http://ecdc.europa.eu/en/activities/microbiology/biosafety/Documents/101117_Bioriskproject_Description.p
df. 

ECDC. Laboratory networks and biosafety communities. How to make biosafety pan-European? Available 
from: http://ecdc.europa.eu/en/publications/Publications/1108_MER_Biosafety.pdf. 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

10. 

11. 

12. 

13. 

14 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Appendix 

The following checklist provides criteria for the planning or overhaul of BSL3 laboratories [1,6,8]. 

Checklist for BSL3 laboratories 

1. 
2 
3. 

4. 

The BSL3 laboratory should be housed in a solid building, ideally separated from other disciplines. 
The BSL3 laboratory should be separated from other (BSL2) laboratories. 
The BSL3 laboratory can only be entered via an anteroom. 
Floors, walls, doors and working surfaces should be non-absorbing, resistant to acids, bases and 
decontaminants, easy-to-clean, and without sections that are hard to access. Seams, gaps and cracks should 
be completely caulked/grouted to seal them.  
The floor should be liquid-tight (higher skirting, welded seams).  
Doors should be self-closing. 

5. 
6. 
7.  Windows should be sealed so they cannot be opened and are air-tight. 
8. 

The entrance door should have a window to monitor the BSL3 laboratory.  

Airflow 

9. 

10. 

11. 

12. 

13. 

14. 

15. 

16. 

Negative pressure must be kept in the anteroom and the laboratory (minimum pressure difference of 15 Pa, 
e.g. -15 Pa in the anteroom and -30 Pa in the laboratory).  
The negative pressure needs to be monitored constantly and displayed outside the laboratory, preferable next 
to the entrance. 
If the negative pressure goes out of range, an audio-visual alert should be triggered in the anteroom and the 
laboratory. 
Air from the laboratory and the anteroom should be extracted via an independent air duct with a HEPA filter. 
The air intake duct does not need to contain a HEPA filter, but should have a one-way valve to prevent any 
backflow in case the negative pressure is not maintained. 
The ventilating system must have an emergency off-switch to prevent a build-up of positive pressure in the 
laboratory if the extraction system fails. 
The ventilating system for a BSL3 laboratory should be completely independent and separate from other 
ventilation systems to prevent cross-contamination. 
There should be a minimum of six to 12 complete air exchanges per hour in a BSL3 laboratory. 
The air intake duct should be separate from the exhaust duct to prevent airflow contamination between the 
two ducts. 

Entrance and access 

17. 

18. 

The entrance to the BSL3 laboratory should be marked with a biohazard sign, information on the containment 
level, details of responsible staff members and biosafety office (including telephone numbers). 
Access to a BSL3 laboratory should be restricted to authorised staff members and controlled by key 
cards/electronic passes. 

19.  An uninterruptible power supply should provide emergency power. 

20. 

If staff technicians are allowed access, they should use personal protective equipment and be supervised by 
regular laboratory staff. Work should be carried out in the early morning when no viable cultures are being 
processed and the laboratory is relatively safe after multiple air exchanges during the night and UV treatment. 
Equipment touched by staff technicians has to be disinfected with 80% ethanol. Maintenance personal should 
be subject to regular occupational health checks. 

21.  Depending on the size of the working space, there should be a sealed emergency exit. 

Anteroom 

22. 

23. 

24. 

25. 

26. 

A door interlock system should be used to prevent the simultaneous opening of doors, thus preventing 
leakage of potentially contaminated air from the BSL3 lab to the corridor. It should be possible to overrule this 
system. 
The anteroom is normally considered a part of the BSL3 area because the anteroom and the laboratory have 
the same ventilating system, but in fact the anteroom is a transition zone between uncontaminated and 
potentially contaminated areas. It is therefore recommended that the anteroom is split into two parts: an 
unclean and a clean zone. The two zones should be clearly marked, e.g. by a laboratory bench. 
Some laboratories only have a small anteroom that is too small to be divided into two zones. If this is the 
case, laboratory coats should be left in the BSL laboratory. 
The anteroom should have a soap dispenser, an alcohol dispenser, a sink and a disposable hand towel 
dispenser. The dispensers as well as the faucet/tap should be hands-free. 
The waste container and the container for worn lab coats should be sealable. Coats have to autoclaved before 
being laundered. Towels are considered relatively harmless and do not need to be autoclaved. 

15 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

27.  An emergency eyewash facility should be installed near the sink. 

Checklist for BSL3 laboratories 

Biological safety cabinets 

Checklist for BSL3 laboratories 

28. 

29. 

30. 

31. 

Class I and II biological safety cabinets are acceptable. For maximum containment at the source, the 
installation of a Class III biological safety cabinet may be considered, although this would result in ergonomic 
disadvantages. 
The biological safety cabinet should be positioned in the laboratory so that airflow would not be disturbed by 
personnel or open doors. A Class III biological safety cabinet is not affected by this. 
Air extracted from a biological safety cabinet can be discharged in three ways: 
1. Air can be recirculated to the room, which is not advisable because of possible biological safety cabinet filter 
leaks which then would introduce contaminated air to the laboratory. This is not just a hypothetical risk, 
especially when biological safety cabinets are not well-maintained. 
2. The biological safety cabinet features a continuous airflow connection with a bypass for air treatment. 
3. With a ‘thimble’ or ‘canopy hood’, extracted air can be recirculated to the room or discharged to the outside 
of the building via a dedicated duct or through the main extraction system. 
When a biological safety cabinet is switched on, it also contributes to the negative pressure in the laboratory. 
However, only options 2 and 3 ensure that the negative pressure is still maintained when the safety cabinet is 
off. 
Biological safety cabinets have to be tested and certified at least once a year. Between maintenance intervals 
safety cabinets are decontaminated by being fumigated with formaldehyde gas.  

Digitalisation of information 

32. 

Any paper-based communication between the BSL3 laboratory and the area outside the laboratory should be 
avoided. Instead, a computer-based laboratory management information system should be used. 

Waste 

33.  Containers for BSL3 waste should be solid, unbreakable, closable and autoclavable. 

34. 

A BSL3 laboratory should be equipped with an autoclave to decontaminate BSL3 waste. 
An autoclave with openings toward the laboratory and the hallway is ideal, as loading of BSL3 occurs directly 
from the BSL3 containment area. 
A stand-alone autoclave inside the BSL3 laboratory is also acceptable, provided there is an adequate solution 
to deal with the contaminated steam/condensate. 
If both options are not possible, an autoclave in the vicinity of the BSL3 laboratory (same building) is 
acceptable, but containers need to be leak-proof and should only be moved under the supervision of the BSL3 
laboratory, without any intermediate storage. 

Wastewater 
35. 

If the BSL3 laboratory has no sink, liquid waste has to be inactivated in an autoclave. 
If a sink is to be installed in a BSL3 laboratory, care should be taken that wastewater is not discharged in the 
public sewer system. Instead, wastewater should be collected in a dunk tank and inactivated (heat, chemicals) 
before it is discharged. 
Although the anteroom is officially considered part of the BSL3 laboratory, the risk of contamination by BSL3 
microorganisms is considered to be so low that wastewater does not have to be decontaminated. 

36. 

37. 

16 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

2 Quality assurance 

Daniela Homorodean, Dimitrios Papaventsis, Tiina Kummik, Vibeke Østergaard Thomsen 

Revised by Daniela Homorodean (2015) 

2.1 Background and principles 

National tuberculosis programmes are to be supported by laboratories that provide quality-assured and reliable results. 
Several European standards (ISO 17025, ISO 15189, ISO 9001) are dedicated to the management of quality assurance 
(QA) [1]. 

Quality assurance covers a number of distinct procedures that help to improve the quality of test procedures and 
therefore the confidence in national TB programmes. National policies regarding the quality of laboratory results 
constitute an essential component of national tuberculosis programmes, and provision of sustainable high-quality services 
is one of the key roles of any NRL. Guidance for national tuberculosis programmes and NRLs on establishing a 
standardised assessment system for the laboratory network focused on microscopy, was published by GLI (Global 
Laboratory Initiative), and proposed eleven standards for TB Microscopy Network Accreditation [2]. It is recommended 
that every laboratory develops, establishes and strictly follows quality assurance procedures for tests used on patients’ 
specimens/isolates. Obviously, quality can be equally good in laboratories with or without a formal QA system, but 
adherence to standards is helpful in identifying problems and the improvement of quality in a systematic manner. 

For laboratories, the formal standards adopted by the majority of European countries are the European standards: ISO 
17025 (General requirements for the competence of testing and calibration laboratories), ISO 15189 (Medical laboratories 
– particular requirements for quality and competence), and ISO 9001 (Quality management systems – Requirements). In 
2012, the revised version of ISO 15189 (Medical laboratories - Requirements for quality and competence) was issued, 
replacing the second edition (ISO 15189:2007) [1]. Accreditation by the two former standards addresses the quality 
system and provides a technical assessment, in contrast to certification by ISO 9001, which addresses the quality system 
only.  

ISO 17025 and ISO 15189 are very similar in their specific requirements. ISO 17025 emphasises the needs of customers, 
whereas ISO 15189 emphasises the need of patients and clinicians. Accredited laboratories often only have ISO 17025 
implemented, as ISO 15189 was only published in 2003. The decision to implement one or the other standard may be 
based on local and national requirements, the status of a health laboratory (commercial or public), proximity to clinical 
departments (diagnostic laboratory, reference laboratory) and the needs of other laboratories at the institute (due to 
accreditation fees). 

17 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Table 2. Overall scope of ISO 17025 and ISO 15189 

ISO 17025. General requirements for the competence 
of testing and calibration laboratories 

ISO 15189:2012 Medical laboratories - 
Requirements for quality and competence 

‘ISO/IEC 17025:2005 specifies the general requirements for 
the competence to carry out tests and/or calibrations, 
including sampling. It covers testing and calibration 
performed using standard methods, non-standard methods, 
and laboratory-developed methods. 
It is applicable to all organisations performing tests and/or 
calibrations. These include, for example, first-, second- and 
third-party laboratories, and laboratories where testing 
and/or calibration forms part of inspection and product 
certification. 
ISO/IEC 17025:2005 is applicable to all laboratories 
regardless of the number of personnel or the extent of the 
scope of testing and/or calibration activities. When a 
laboratory does not undertake one or more of the activities 
covered by ISO/IEC 17025:2005, such as sampling and the 
design/development of new methods, the requirements of 
those clauses do not apply. 
ISO/IEC 17025:2005 is for use by laboratories in developing 
their management system for quality, administrative and 
technical operations. Laboratory customers, regulatory 
authorities and accreditation bodies may also use it in 
confirming or recognizing the competence of laboratories. 
ISO/IEC 17025:2005 is not intended to be used as the basis 
for certification of laboratories.’ [1] 

In this new version, some chapters have been 
renamed and some requirements are more detailed 
both in management and technical requirements. 
There are new normative sections (Reporting and 
Release of results), and annexes B and C from the 
former became new sections (Laboratory information 
management and Ethical conduct, respectively). 

Laboratory accreditation/certification (by a national body providing official recognition of laboratory quality) 
according to these standards recognises the professional competence of the laboratory and provides an official 
indicator of high performance standards. Central terms are given in Table 3 and further terms are defined in the 
publication ‘International vocabulary of metrology – basic and general concepts and associated terms’ (VIM) [3] 
and the ‘IUPAC Compendium of Chemical Technology – the gold book’ [4]. This chapter outlines the most 
important requirements from ISO/IEC 17025 and ISO 15189:2012. It takes into account the special requirements 
imposed by the medical environment and the contribution of medical laboratory services to patient care. It 
recognises that medical laboratories not only test patient samples, but also offer advisory, interpretative and 
educational services. The full text of these standards is available for purchase online [1]. 

Table 3. Central terms and abbreviations in quality assurance 

Quality 
assurance 
(QA) 

A system for continuously improving and monitoring the reliability, efficiency and 
clinical utilisation of laboratory tests. Quality control, quality improvement and method 
validation are integral components of quality assurance. 

A process of regular performance checks to ensure that a method is performing as expected. 
Internal quality assessment (IQA) includes controls tested in parallel with specimens/isolates. This 
evaluates the precision and accuracy of the test results, the performance of the test reagents and 
how well laboratory staff perform when carrying out the test. 
External quality assessment (EQA) or proficiency panels are specimens/isolates received from an 
independent organisation in order to assess the performance of the participating laboratory. Inter-
laboratory comparison is an alternative when proficiency panels are not available and includes the 
exchange of specimens/isolates with other laboratories (usually at least three) that perform the 
same tests. 
Validation is the ‘confirmation by examination and the provision of objective evidence that the 
particular requirements for a specific intended use are fulfilled.’ (ISO 17025) 
For each test, key indicators should be identified and followed routinely in order to monitor trends 
(early detection of deviations). 

Quality 
assessment 

Validation 

Key 
indicators 

2.2 Selection and implementation of tests 

The laboratory should use testing methods that meet the needs of the customer and include procedures for 
sampling, handling, transport and the storage and preparation of specimens/isolates. Methods should apply 
international, regional, or national standards by reputable technical organisations, from scientific journals, or as 
specified by a kit/equipment manufacturer. Laboratory-developed methods, or methods adopted by the laboratory 

18 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

may also be used if appropriate and validated. The laboratory should confirm that it can properly perform the 
methods before introducing the tests [6,7]. 

2.3 Validation 

Non-standard methods, laboratory-developed methods, standard methods used outside their intended scope, 
modifications of standard methods, and changes in established methods should be validated. Validation is the 
‘confirmation by examination and the provision of objective evidence that the particular requirements for an 
intended use are fulfilled’ (ISO 17025). Validation includes specification of written requirements, determination of 
the assay characteristics, checking that the requirements are fulfilled by the assay and a statement on the validity. 
For standardised methods it is only necessary to validate that the method works locally as expected. Validation is a 
relative process: sensitivity and specificity of diagnosis is calculated in relation to a standard, verified procedure. 
Part of the validation may have been carried out by the manufacturer or by other laboratories. Since the 
introduction of the ‘in vitro diagnostic directive’ (IVD) 5] in 2003, manufacturers have been legally bound to carry 
out extensive validation. In this case, the validation can be a reduced equivalent, but the laboratory still has to 
verify that the method works locally as expected. In all cases, the laboratory should have access to documentation 
equivalent to a full validation and assess whether the validation is relevant to the use and whether the 
requirements are fulfilled.  

It is not possible to recommend one validation method for all tests. Validation can be done using: 

 
 
 
 

a comparison of results achieved with other methods 
inter-laboratory comparisons 
a systematic assessment of factors influencing the result; and 
an assessment of the uncertainty of the results, based on a scientific understanding of the theoretical 
principles of the method and practical experience. 

An overview of validation principles can be found in Westgard (2008) [6] and Westgard (2010) [7]. In addition, the 
following factors may be assessed: 

 
 
 
 
 
 
 
 

coefficients of variation 
uncertainty of results 
detection limit 
sensitivity 
specificity 
linearity 
limit of repeatability and/or reproducibility; and 
robustness. 

In many cases, the range of values has been simplified due to lack of information. 

2.4 Control and trend monitoring by key indicators 

Appropriate internal quality assessments (IQAs) should be selected and run in parallel with specimens/isolates in 
order to monitor routine performance regularly (e.g. control slides for microscopy). Reference strains can be purchased 
from different strain collections [1,2,3,5,6]. 

Key indicators can be used to monitor performance trends over time and allow early identification of deviations (e.g. 
proportion of contaminated cultures or proportion of inconclusive IGRA results over a certain time period). The NRL from 
each country provides guidelines for IQAs in accordance with the ISO standard requirements, the methods used and 
local conditions (infrastructure, workload, equipment and staff). Examples of IQAs can be found in Chapters 3 to 7. 

External quality assessment (EQA) programmes are essential parts of quality assurance. Programmes of relevance for 
mycobacteriology laboratories are available through INSTAND e.V., UK NEQAS, US CDC, LabQuality and the WHO 
supranational TB reference laboratories, to which all national TB reference laboratories have links. If EQA programmes for 
a test are not available, exchanges with other laboratories can be arranged. A minimum of three laboratories should 
participate; however, EQA programmes do not replace IQA [2].  

2.5 Physical and environmental conditions 

The basic set-up of a laboratory (energy supply, lighting, environmental conditions) should be conducive to its 
testing activities. Physical and environmental conditions that can negatively affect results should be monitored and 
documented. Areas with incompatible activities should be separated (e.g. primary specimens and mycobacterial 
isolates and pre- and post-amplification areas) and precautions should be taken to prevent cross-contamination. 
Access to and use of laboratories must be controlled if this will affect the quality of tests. Measures should also be 
taken to ensure good housekeeping in the laboratory, thus improving biosafety (Chapter 1) [1,2,3,5,6]. 

19 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

2.6 Equipment 

Equipment and related software must achieve the required level of accuracy and comply with specifications 
relevant to the tests. Procedures for handling, storage, use and maintenance should ensure the proper functioning 
of the equipment and prevent contamination or deterioration. Equipment with a measuring function must be 
calibrated initially and regularly thereafter. Procedures should be in place to ensure that equipment suspected of 
malfunction is not used until checked.  

Records should be maintained for critical equipment: manufacturer’s name; identification and serial number; 
compliance checks; location; manufacturer’s instructions; results; reports; certificates of all 
calibrations/adjustments; acceptance criteria; date of next calibration; maintenance plan; registrations of damage, 
malfunction, modification or repair. The equipment itself should be labelled with the status of calibration and date 
of last and next recalibration [1,2,3,5,6]. 

2.7 Management and staff 

Managerial and technical staff must be authorised to carry out tests to the required standards. All necessary 
resources must be available to them. Management and staff should be free of any conflicts of interest and key 
personnel should have appointed deputies. One person should be appointed quality officer and laboratory staff 
should understand that quality is everyone’s responsibility. Management must document the competencies of the 
staff to ensure that equipment is properly handled, and that they know how to carry out testing, assess and 
approve results and sign reporting forms. In some countries, formal authorisation may apply to some staff 
members. Staff members giving guidance or interpreting results should be knowledgeable about the applied 
technology and the significance of the results. Ideally, staff should be employed in permanent positions or have 
signed a contract. Job descriptions should be available for managerial, administrative, and technical staff involved 
in testing [7]. 

2.8 Documentation and registration 

Laboratories document their policies and procedures for testing and equipment use (in their local language) to ensure 
the quality of results. All documents must be reviewed and approved by authorised staff before being issued. They 
must also be read and understood by the relevant staff and revised on a regular basis. The use of expired/amended 
documents must be prevented. All documents should be easily accessible. Handwritten corrections and annotations 
should be incorporated quickly into the official version of the document. Handwritten corrections should be dated and 
signed with initials [1,2,3,5,6].  

Procedures for registration of specimens should include specimen identification, access, archiving, maintenance, and 
disposal. Procedures should specify how long registration forms have to be kept on file. Registration forms should be 
clearly legible, accessible, remain confidential to outsiders, and be kept in conditions that prevent damage and loss. 
Calculations and data transfers should be subject to appropriate and systematic checks. Registration documents 
should make it possible to replicate the entire testing process. When errors are identified, the correct information 
should be entered next to the error, without overwriting the incorrect entry, and then signed or initialled and dated by 
the staff member who corrected the information.  

Electronic data must be protected (entry; storage, including back-up, access, transmission, and processing) according 
to the national data protection policy. In addition, in-house developed computer software ought to be documented 
and validated.  

2.9 Sampling guidance, review of requests and service to 
customers 

The laboratory provides the customer with standardised operating procedures (based on existing guidelines) for 
sampling that are easily accessible at the sampling location (e.g. online). The sampling guidelines address all factors 
that need to be controlled in order to ensure the validity of the test (e.g. specimen quality and volume, specimen 
number, transportation time and temperature). When specimens are sub-optimal or unacceptable for testing, the 
results report should indicate this and/or this should be communicated to the appropriate staff members [1,2,3,5,6].  

Procedures must be implemented for the review of requests, tenders and contracts for testing according to the 
national guidelines. For routine diagnostics, recommendations from the laboratory and the completed request form is 
sufficient. The laboratory will identify customer needs, including guidance and analysis of results. In the event of 
major deviations/delays, the customer should be informed. 

20 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

2.10 Subcontracting, services and supplies 

It is the responsibility of the laboratory to ensure that all work undertaken by subcontractors is completed to meet the 
required standards. Examples are the calibration of equipment or second-line drug susceptibility testing of M. 
tuberculosis at another laboratory. There is a need for policies and procedures for services and supplies that directly 
influence diagnostic quality: procedures cover the purchase, receipt and storage of reagents, as well as compliance of 
supplies with standards and regulations. The laboratory is advised to assess suppliers of critical services and supplies. 
CE-marked reagents are produced according to the EU directive and are in compliance with national regulations. 

2.11 Complaints, errors and corrective actions 

Policies and procedures regarding complaints, deviations and corrective actions should be established and 
registered. When errors are identified, the significance should be assessed and corrective actions implemented. 
The customer should be informed and the results corrected or withdrawn. It should then be assessed when the 
testing can be resumed. If the assessment indicates that the error could happen again (systematic error), 
corrective action must be taken immediately and its effect controlled. All corrective actions have to be authorised 
first [1,2,3,5,6]. 

2.12 Improvements 

Senior management should be committed to developing, implementing and improving the quality assurance 
system. The laboratory should revise the quality system regularly by establishing a quality policy and formulating 
quality objectives. Improvement methods include preventive actions, assessments of complaints and deviations, 
corrective actions (as above), observations from internal audits, data analyses and management evaluations. 
Internal audits should be carried out annually by trained, qualified staff not involved in the audited activities. 
Management reviews carried out annually assess the suitability of policies and procedures, staff reports, results 
from internal audit(s), corrective and preventive actions, assessments from external parties, results from external 
proficiency panels or inter-laboratory comparisons, changes in workload, customer enquiries, complaints and other 
relevant factors [1,2,3,5,6]. 

2.13 Reporting and releasing results 

It is essential that the results of each test are reported accurately, clearly, unambiguously and objectively. Each 
report includes a title, the name and address of the laboratory, the unique identification of the test report (all 
pages), an end-of-report message (or other indicator at the end of the report), the name and address of the 
customer, the method used, a description of specimens/isolates (including sampling date), patient identification, 
specimen type, date of receipt, test result, release date and name of the person(s) authorising the report [1,2,6,7].  

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

International Organization for Standardization. ISO Standards. Geneva: ISO; 2011. Available from: 
http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=39883 and 
http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=42641. 

TB Microscopy Network Accreditation – An assessment tool. First English Edition, October 2013. Available 
from: http://www.stoptb.org/wg/gli. 

International Organization of Legal Metrology (OIML), Joint Committee for Guides in Metrology. 
International vocabulary of metrology – basic and general concepts and associated terms (VIM). Paris: 
International Organization of Legal Metrology; 2007. [accessed 28 July 2015.] Available from: 
http://www.oiml.org/en/files/pdf_v/v002-200-e07.pdf/view. 

International Union of Pure and Applied Chemistry. IUPAC Compendium of chemical terminology – the gold 
book [Internet]. Research Triangle Park, NC: IUPAC; 2005-2009 [accessed 28 July 2015.] Available from: 
http://goldbook.iupac.org. 

Directive 98/79/EC of the European Parliament and of the Council of 27 October 1998 on in vitro diagnostic 
medical devices. Available from: https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:31998L0079. 

Westgard, JO. Basic method validation. 3rd edition. Madison, WI: Westgard QC; 2008. 

Westgard, JO. Tools, technologies and training for healthcare laboratories [Internet]. Madison, WI: 
Westgard QC; 2009 [accessed 28 July 2015]. Available from: http://www.westgard.com. 

21 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

3. The diagnosis of latent TB infection 

Dimitrios Papaventsis and Vladyslav Nikolayevskyy 

Revised by Dimitrios Papaventsis and Vladyslav Nikolayevskyy (2015) 

3.1 Background and principles 

Most people who are initially infected with Mycobacterium tuberculosis do not develop active tuberculosis. This 
state (when a person infected with the TB bacillus has not developed active TB) is called latent TB infection (LTBI) 
[1]. It is characterised by persistence and a low-rate multiplication of viable M. tuberculosis bacilli within 
macrophages and evidence of an immune response against the bacterium, but without clinical manifestation and 
radiological and bacteriological evidence of active disease. One third of the world’s population (almost two billion 
people worldwide) is estimated to be latently infected with tuberculosis – an enormous reservoir of potential 
tuberculosis cases [2]. Latency can be maintained for the lifetime of the infected person. 

Primary infection leads to active disease in 10% of infected individuals, mostly within two years of infection [3]. 
When the host immune response weakens (e.g. through HIV infection, malnutrition, the use of steroids/other 
immunosuppressive medications, or advanced age), reactivation of latent infection may occur [4]. 

Being non-infectious, those latently infected with the TB do not pose an immediate risk of TB transmission. 
Detection of the LTBI, however, is an important means of global TB control and constitutes a major part of the 
WHO Global Plan to Stop TB [5]. Putting people with LTBI on chemoprophylaxis significantly reduces their risk of 
developing active TB. An ideal test for LTBI diagnosis should meet the following criteria [5]:  

 
 
 
 
 

High sensitivity in all populations at risk; 
High specificity regardless of BCG vaccination and infection with environmental mycobacteria;  
Reliability and stability over time; 
Objective criteria for positive result, affordability and easy administration; 
Ability to identify recently infected individuals with increased risk of progression to active TB.  

There are currently two groups of tests for LTBI diagnosis: tuberculin skin tests (TST) and interferon-γ release 
assays (IGRA).  

3.1.1 Immune response to M. tuberculosis 

The immune response to M. tuberculosis is multifaceted. Immunological mechanisms involved in maintaining a 
latent infection are complex, but are clearly necessary to prevent reactivation [1]. When the human host is infected 
by M. tuberculosis there are three potential outcomes (Figure 2): 

Spontaneous healing 

Latency. In most cases, mycobacteria are initially contained and disease develops later as a result of 
reactivation. The granuloma that forms in response to M. tuberculosis consists of macrophages, which can 
differentiate into epithelioid macrophages or multinucleate giant cells, CD4 and CD8 T-cells, and B cells. The 
T-cells produce interferon-γ, which activates macrophages. CD8 T-cells can lyse infected macrophages or 
kill intracellular bacteria. Tumour necrosis factor (TNF) is produced by macrophages and T-cells. Dendritic 
cells are also present, and a mature granuloma is surrounded by fibroblasts. M. tuberculosis is present 
within the macrophages and extracellularly.  

Development of tuberculosis directly after infection in the immunocompromised host: On depletion of CD4 T 
cells (e.g. during HIV infection), the granuloma does not function as well, production of interferon-γ may 
decrease, and macrophages are less activated. As a result, M. tuberculosis begins to multiply and active TB 
develops. In the case of TNF neutralisation, the cells within the granuloma are no longer as tightly 
clustered, perhaps owing to chemokine or adhesion-molecule dysregulation. In addition, the macrophages 
are not as activated. These defects lead to a disorganised granuloma that is less able to control infection 
and greater immunopathology [1]. 

 

 

 

22 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Figure 2. Potential outcomes of human host infection by M. tuberculosis 

Reprinted by permission from Macmillan Publishers Ltd: Nature Reviews Immunology, S. Kaufmann, How can immunology 
contribute to the control of tuberculosis? 2001 Oct;1 [17] 

Although the host response is essential to controlling the infection, M. tuberculosis participates in the establishment 
of latency by using various strategies to evade elimination by the host [1]. M. tuberculosis can subvert various anti-
mycobacterial functions of macrophages. Once engulfed, M. tuberculosis ends up in a phagosome, the maturation 
of which is arrested at an early stage [17]. Within the phagosome, M. tuberculosis is subject to the anti-
mycobacterial effect of reactive nitrogen intermediates (RNI) [1]. M. tuberculosis inhibits phagosomal acidification 
and prevents fusion with lysosomal compartments. The bacilli can also inhibit the MHC class II-dependent antigen 
presentation pathway.  

3.2 The tuberculin skin test (TST) 

First introduced in 1890, the TST is an intradermal injection of purified protein derivative (PPD). The PPD is a crude 
antigenic mixture, shared among M. tuberculosis, M. bovis, and other non-tuberculous mycobacteria (NTM) [6]. 
The test measures in vivo a delayed-type hypersensitivity reaction based on immunological recognition of 
mycobacterial antigens in exposed individuals. Mycobacterial antigens are injected below the epidermal layer, 
causing infiltration of antigen-specific lymphocytes and the elaboration of inflammatory cytokines. This 
inflammatory reaction results in the characteristic indurated area at the site of injection.  

Until recently, the TST was the only tool for detecting LTBI. Limitations of the test include: 

 
 

 
 
 
 

a high proportion of false positive and false negative results 
difficulty in separating true infection from the effects of BCG vaccination and non-tuberculous mycobacteria 
infection 
technical problems in administration 
immune response boosting after repeated TST 
complicated and subjective interpretation; and 
a need for a second visit. 

3.3 Interferon-γ release assays (IGRAs) 

3.3.1 Introduction 

The QuantiFERON-TB Gold (QFT-G, by Qiagen GmbH, Hilden, Germany) and the T-SPOT (by Oxford Immunotec 
Limited, Abingdon, UK) are two in-vitro ex-vivo tests for measuring cell-mediated immune responses (CMIR) to 
peptide antigens that simulate mycobacterial proteins. These antigens, ESAT-6, CFP-10 and TB7.7 (p4) (used only 
in QFT-G) are absent from all BCG strains and from most non-tuberculous mycobacteria with the exception of M. 

23 

 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

kansasii, M. szulgai and M. marinum [7-9]. Individuals infected with M. tuberculosis complex organisms (M. 
tuberculosis, M. bovis, M. africanum, M. microti, M. canetti) have mononuclear cells in their blood that recognise 
these mycobacterial antigens. This recognition process leads in vitro to the stimulation and secretion of Interferon-
γ (IFN-γ) from sensitised T-cells. The detection and subsequent quantification of IFN-γ, measured by enzyme-
linked immunoassay (QuantiFERON) or enzyme-linked immunospot (T-SPOT), forms the basis of these tests [10]. 
Both tests are intended for use in conjunction with risk assessment, radiography, and other medical and diagnostic 
evaluations. Potential advantages of IGRAs over TST include: greater sensitivity; higher specificity (less influenced 
by BCG vaccination and non-tuberculous mycobacteria infection; less influence by technical problems in 
administration and interpretation and the need for only one visit.  

3.3.2 Current national guidelines and the clinical use of IGRAs 

With the growing evidence, many national guidelines for LTBI diagnosis now include IGRAs although most 
countries continue to recommend and use TST. A recent review [18], based on thirty-three guidelines and policy 
papers from 25 countries and two international organisations, demonstrated considerable diversity in the 
approaches. Guidelines are predominantly available in high-income countries with established LTBI screening 
programmes. Four approaches are generally adopted: 

 

 
 
 

two-step approach of TST first, followed by IGRA, either when the TST is negative (to increase sensitivity, 
mainly in immunocompromised individuals), or when the TST is positive (to increase specificity, mainly in 
BCG-vaccinated individuals); 
either TST or IGRA, but not both; 
IGRA and TST together (to increase sensitivity) 
IGRA only, replacing the TST.  

There is also a trend towards using IGRAs alone prior to anti-TNF-α therapy. Some guidelines are still not 
proposing IGRA use in children under five years of age. Most of the current guidelines do not use objective, 
transparent methods to grade evidence and recommendations, and rarely disclose conflicts of interests. Existing 
national guidelines on LTBI diagnosis in EU/EEA countries are listed in Table 4. 

Table 4. List of national LTBI diagnosis guidelines 

Country 

Guideline 

Schmidgruber B. Guidelines for the diagnosis of latent tuberculosis in canton Vienna; 
2011; Gesundheitsdienst (Department of Public Health) of Vienna; Austria. 
Markova R. Guidelines for the diagnosis of latent tuberculosis in Bulgaria; 2011; Dept. 
Immunology and Allergology, National Centre of Infections and Parasitic Diseases; 
Sofia, Bulgaria. 
Katalinic-Jankovic V. Guidelines for the diagnosis of latent tuberculosis in Croatia; 
personal communications with Vera Katalinic-Jankovic. 2011; Croatia National Institute 
of Public Health; Zagreb, Croatia 
Czech Thoracic Society. Recommendation of Czech Thoracic Society for QuantiFERON-
TB Gold test; 2005; Research Institute for Tuberculosis and Respiratory Diseases; 
Prague, Czech Republic. 

Diagnos af tuberkulose, 2011; Dansk Lungemedicinsk Selskab, Denmark 

Suositus tuberkuloosin kontaktiselvityksen toteuttamiseksi, 2011; Terveyden Ja 
Hyvinvoinnin Laitos, Finland 
Test de détection de la production d'interféron-y pour le diagnostic des infections 
tuberculeuses, 2006; Haute Autorité de Santé, France 
Neue Empfehlungen für die Uµgebungsuntersuchungen bei Tuberkulose 
Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose. New Recommendations 
for Contact Tracing in Tuberculosis German Central Committee against Tuberculosis. 
Germany 
Guidelines on the Prevention and Control of Tuberculosis in Ireland, 2010; Health 
Protection Surveillance Centre, Ireland 
Aggiornamento Delle Raccomandazioni Per Le Attività Di Controllo Della Tubercolosi: 
Gestione dei contatti e della tubercolosi in ambito assistenziale, 2009; Ministero del 
Lavoro della Salute e delle Politiche Sociali, Italy 
Interferon Gamma Release Assays bij de diagnostiek van tuberculose, 2011; 
IGRA-werkgroep Commissie voor Praktische Tuberculosebestrijding, Netherlands 

Tuberkuloseveilederen som e-bok, 2011; Folkehelseinstituttet, Norway 

Austria 

Bulgaria 

Croatia 

Czech Republic 

Denmark 

Finland 

France 

Germany 

Ireland 

Italy 

Netherlands 

Norway 

24 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Country 

Guideline 

Poland 

Portugal 

Slovakia 

Spain 

Switzerland 

United Kingdom 

Zalecenia postępowania w zapobieganiu i leczeniu gruźlicy u chorych leczonych 
antagonistami TNF-α / Recommendations for prophylaxis and management of 
tuberculosis in patients treated with TNF-α antagonists, 2008; Poland 
Tuberculose Latente: Projecto de expansão dos testes IGRA, 2010; 
Programa Nacional de Luta Contra a Tuberculose (PNT), Portugal 
Slovakian Guidelines on Latent Tuberculosis Testing, 2010; 
Ministerstva Zdravoníctva Slovenskej Republiky, Slovakia 
Consensus Document on the Diagnosis, Treatment and Prevention of Tuberculosis, 
2010; Spanish Society of Pneumology and Thoracic Surgery (SEPAR), Spain 
Handbuch Tuberkulose (Rohfassung), 2011; Kompetenzzentrum Tuberkulose, 
Switzerland 

Tuberculosis: NICE Guideline, 2011; NICE, UK 

Information included in the different national guidelines and recommendations suggests that IGRAs are 
increasingly being recommended, primarily in low-incidence settings, as they offer a higher specificity combined 
with logistical advantages [19]. TST is still favoured in high-incidence and low-resource settings. 

In general, evidence suggests that screening for LTBI (using both TST and IGRA) should ideally be confined to 
those who are at sufficiently high risk of progressing to disease and who will benefit from chemoprophylaxis should 
they test positive. 

The clinical use of IGRAs in different groups has been recently reviewed and policy papers have been published by 
international organisations including WHO and ECDC [20-23]. WHO generally discourages use of IGRAs and 
recommends using TST, but only in low- and middle-income settings, regardless of HIV status. The ECDC approach 
is based on TB incidence. In high-incidence settings, the ECDC suggests not to use IGRAs to diagnose LTBI since 
the focus of prevention and control is on identifying and treating active TB cases. In low-incidence settings a two-
step approach is suggested. For active TB diagnosis, ECDC suggests that IGRAs should not be a replacement for 
standard diagnostic methods and generally do not have an added value in most clinical situations, when combined 
with standard methods for diagnosing active TB. However, in certain clinical situations (e.g. patients with 
extrapulmonary TB, patients who test negative for acid-fast bacilli in sputum and/or negative for M. tuberculosis 
after culture, TB diagnosis in children, or in the differential diagnosis of infection with non-tuberculous 
mycobacteria), ECDC suggests that IGRAs could contribute supplementary information as part of the diagnostic 
process and laboratory management. Overall, the contact tracing practices in adults appear to suggest a clear 
trend towards an increased use of IGRAs, especially in low-incidence countries, mostly as a two-step strategy [18]. 

3.3.3 Predictive value of IGRA for progression to active TB 

Existing evidence suggests that both TST and IGRA are acceptable but imperfect tests and neither test can 
accurately differentiate between LTBI and active TB, distinguish reactivation from reinfection, or accurately predict 
progression from LTBI to active disease [19]. In a recent meta-analysis [24] based on a combined sample size of 
26 680 individuals and data derived from 15 longitudinal studies it was concluded that neither IGRA nor TST 
accurately predict the risk of developing active TB, although use of IGRAs in certain groups might reduce the 
number of people considered for chemoprophylaxis. 

Overall, evidence currently available suggests that the predictive value of IGRAs for progression to active TB 
disease is low and only marginally (non-significantly) higher than that of the TST [19]. There is also limited 
evidence suggesting that IGRA conversion detected using multiple testing may have a greater predictive value than 
single IGRA results as it may indicate recent infection [25]. With regard to high-risk populations (e.g. HIV-infected 
individuals) there are currently no data suggesting that IGRAs are better in predicting active TB in this group than 
the TST [19,26]. 

To conclude, evidence available to date suggests that both TST and IGRA have limited predictive values and their 
usefulness is restricted to identification of those who would potentially benefit from preventive therapy. Current 
and future studies will help establish the place and role of IGRAs in TB clinical and laboratory management and 
potentially identify novel, highly-predictive biomarkers. 

Existing evidence suggests that both TST and IGRA are acceptable but imperfect tests and neither of the tests can 
accurately differentiate between LTBI and active TB; distinguish reactivation from reinfection, or accurately predict 
progression from LTBI to active disease [19]. In a recent meta-analysis [24] based on a combined sample size of 
26 680 individuals and data derived from 15 longitudinal studies, it was concluded that neither IGRA nor TST 
accurately predict the risk of developing active TB, although use of IGRAs in certain groups might reduce the 
number of people considered for chemoprophylaxis. 

Overall, current evidence suggests that the value of IGRAs for predicting progression to active TB disease is low 
and only marginally (non-significantly) higher than that of the TST [19]. There is also limited evidence suggesting 

25 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

that IGRA conversion detected using multiple testing may have a greater predictive value than single IGRA results 
as it may indicate recent infection [25]. With regard to high-risk populations (e.g. HIV-infected individuals) there 
are currently no data suggesting that IGRAs are better in predicting active TB in this group than the TST [19,26]. 

To conclude, evidence available to date suggests that both TST and IGRA have limited predictive values and their 
usefulness is restricted to identification of those who would potentially benefit from preventive therapy. Current 
and future studies will help establish the place and role of IGRAs in TB clinical and laboratory management and 
potentially identify novel, highly predictive biomarkers. 

3.3.4 IGRA performance and reproducibility 

Performance characteristics (sensitivity and specificity) of the two IGRAs currently available on the market (QFT-G 
and the T-SPOT) have recently been extensively reviewed [19,27,28]. In the absence of a gold standard, surrogate 
markers are used to estimate performance characteristics. Specificity of both assays (>95%) is not affected by 
BCG vaccination and is similar to that of the TST in non BCG-vaccinated individuals; in populations where BCG 
vaccination is administered, specificity of TST is significantly lower (60%). Existing evidence suggests that 
sensitivity of T-SPOT is slightly higher (~90%) than that of QFT-G (~80%) and is usually lower in children and 
immunocompromised individuals.  

IGRAs have certain reproducibility issues and variability can be due to natural sources (immunomodulation and 
functionality of T-cells), manufacturing issues, pre-analytical and analytical deviations. This may require the 
reconsideration of cut-off values and the introduction of borderline zones (especially for the QFT-G assay) which 
might help to improve the reproducibility and diagnostic value of the assays [19]. 

3.3.5 Procedure 1: QuantiFERON-TB Gold and QuantiFERON-TB Gold 
PLUS 

The QuantiFERON-TB Gold (QFT-G) and QuantiFERON-TB Gold PLUS (QFT-GP) made by Qiagen GmbH, Hilden, 
Germany)1. 

General principles 
The QuantiFERON-TB Gold IT system uses blood collection tubes that contain antigens representing specific M. 
tuberculosis proteins or controls. After blood collection (nil control, TB antigen and a mitogen tube for QFT-G and 
nil control, two antigen tubes, and a mitogen tube for QFT-GP), tube incubation at 37°C ± 1°C for 16 to 24 hours 
follows. When incubation is complete, the tubes are centrifuged, plasma is harvested and the amount of IFN-γ 
produced is measured by ELISA. Results for test samples are reported in International Units (IU) relative to a 
standard curve prepared by testing dilutions of the secondary standard supplied by the manufacturer. The effect of 
heterophile antibodies is minimised by adding normal mouse serum to the green diluent and using F(ab’)2 
monoclonal antibody fragments as the IFN-γ capture antibody coated to the microplate wells. 

Baseline epidemiological data 
Before performing the QuantiFERON-TB Gold IT test, baseline epidemiological data should be recorded: name, full 
address, contact information, gender, occupation, place of birth, time since immigration (if applicable), travel 
history, history of BCG vaccination and TST, clinical data (medication uptake, immunosuppression, weight loss, 
night sweats, fever, cough, abnormal chest X-ray (CXR), previous TB treatment/chemoprophylaxis, etc.). Baseline 
data should be recorded on the patient data sheet that accompanies the specimen (see Chapter 3, Appendix 1). 

Safety 
Care should be taken when handling materials of human origin. All blood samples should be considered potentially 
infectious. Handling of blood samples and assay components, their use, storage and disposal should be in 
accordance with procedures defined in appropriate national, state or local biohazard and safety guidelines or 
regulations. Eye protection, gloves and normal laboratory protective clothing should be worn. Correct laboratory 
procedures should be adhered to at all times. 

Materials provided by the manufacturer 
Blood collection tubes 

QFT-G: 

 
 
 

Nil control (grey cap with white ring) 
TB antigen (red cap with white ring) 
Mitogen control (purple cap with white ring). 

1 Descriptions of laboratory procedures are based on the manufacturer’s recommendations (Qiagen) and international safety, 
quality control and laboratory management regulations. QuantiFERON-TB Gold package insert available from: 
http://www.quantiferon.com/irm/content/PI/QFT/PLUS/UK.pdf 

26 

 
 
 
 
                                                                    
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

QFT-GP: 

 
 
 
 

Nil control (grey cap with white ring) 
TB 1 antigen (green cap with white ring) 
TB 2 antigen (yellow cap white ring) 
Mitogen control (purple cap with white ring). 

ELISA components: 

 
 

 
 
 
 
 

Microplate strips coated with murine anti-human IFN-γ monoclonal antibody 
Human IFN-γ standard, lyophilised (8 IU/ml when reconstituted; contains recombinant human IFN-γ, bovine 
casein, 0.01 % w/v thimerosal) 
Green diluent (contains bovine casein, normal mouse serum, 0.01% w/v thimerosal) 
Conjugate 100x concentrate, lyophilised (murine anti-human IFN-γ HRP, contains 0.01% w/v thimerosal) 
Wash buffer 20x concentrate (pH 7.2, contains 0.01 % w/v thimerosal) 
Enzyme substrate solution (contains H2O2, 3,3’,5,5’ tetramethylbenzidine) 
Enzyme stopping solution (contains 0.5M H2SO4). 

Required materials (not provided) 
 
 
 
 
 
 
 
 
 
 
 
 

37°C ± 1°C incubator (with or without CO2) 
Calibrated variable-volume pipettes for delivery of 10 µl to 1000 µl with disposable tips 
Calibrated multichannel pipette capable of delivering 50 µl and 100 µl with disposable tips 
Centrifuge capable of centrifuging the blood tubes at least to 3 000 RCF (g) 
Microplate shaker capable of speeds between 500 and 1 000 rpm 
Deionised or distilled water: 2 l 
Microplate washer (for safety reasons, an automated washer is recommended) 
Microplate reader fitted with 450 nm filter and 620nm to 650 nm reference filter 
Variable speed vortex 
Timer 
Measuring cylinder: 1 or 2 l 
Reagent reservoirs. 

Storage 
 
 

Blood collection tubes: store blood collection tubes at 4°C to 25°C (40°F to 77°F) 
ELISA kit reagents: store kit at 2°C to 8°C (36°F to 46°F). Always protect enzyme substrate solution from 
direct sunlight 
Reconstituted and unused reagents: the reconstituted kit standard may be kept for up to three months if 
stored at 2°C to 8°C. Note the date on which the kit standard was reconstituted; 
The reconstituted 100x conjugate concentrate must be returned to storage at 2°C to 8°C and must also be 
used within three months. Note the date the 100x conjugate was reconstituted 
Working strength conjugate must be used within six hours of preparation 
Working strength wash buffer may be stored at room temperature for up to two weeks. 

 

 

 
 

Methods 
Sample collection and handling 

The contents of the tubes should be thoroughly mixed with the blood. Incubation at 37°C ± 1°C should begin as 
soon as possible and within 16 hours of collection. For best results, the following procedures should be followed: 

For each subject collect 1 ml of blood by venipuncture directly into each of the QuantiFERON-TB Gold IT blood 
collection tubes. If the level of blood in any tube is not close to the indicator line, it is recommended that another 
blood sample be obtained. Under- or over-filling of the tubes outside of the 0.8 to 1.2 ml range may lead to 
erroneous results. High altitude (HA) tubes should be used at altitudes between 1000 and 2000 meters. Blood can 
also be collected using a syringe and 1 ml transferred to each of the three tubes, ensuring appropriate safety 
procedures. Alternatively, blood may be collected in a single generic blood collection tube and then transferred to 
QFT tubes. The generic collection tube must only contain lithium heparin as an anticoagulant, other anticoagulants 
such as EDTA may interfere with the assay. 

Thorough mixing is required to ensure complete integration of the tube’s contents into the blood. Mix the tubes by 
shaking vigorously for five seconds (ten times). 

Label the tubes appropriately.  

Prior to incubation, maintain tubes at room temperature (22°C ± 5°C). Do not refrigerate or freeze the blood 
samples.  

Perform specific tasks within set times. 

27 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Stage One: Incubation of blood and harvesting of plasma 

The tubes will have to be re-mixed if the blood is not incubated immediately after collection. 

Incubate the tubes upright at 37°C ± 1°C for 16 to 24 hours. No CO2 or humidification incubator is required. 

Following incubation, blood collection tubes may be held between 2°C and 27°C for up to three days prior to 
centrifugation.  

After incubation, centrifuge tubes for 15 minutes at 2000 to 3000 RCF (g). If the cells are not separated from the 
plasma by the gel plug, the tubes should be re-centrifuged at a higher speed.  

Plasma samples can be loaded directly from blood collection tubes into the ELISA plate. 

Alternatively, plasma samples can be stored prior to ELISA, either in the centrifuged tubes or collected into plasma 
storage containers. Plasma samples can be stored for up to 28 days at 2°C to 8°C or below -20°C (preferably less 
than -70°C) for extended periods. 

Stage Two: Human IFN-γ ELISA 

Before use, plasma samples and reagents, except for conjugate 100x concentrate, must be brought to room 
temperature (22°C ± 5°C). Allow at least 60 minutes for equilibration. 

Allow at least two strips on the ELISA frame for the standards and sufficient strips for the number of subjects being 
tested. Remove strips that are not required from the ELISA frame, reseal in the foil pouch, and return to the 
refrigerator for storage.  

Reconstitute the human interferon-γ kit standard with the indicated volume of deionised or distilled water (see 
label; concentration of 8.0 IU/ml). Use the reconstituted kit standard to produce a dilution series of 4 IFN-γ 
concentrations (4.0, 1.0, 0.25, 0 IU/ml). Green diluent serves as the zero standard. 

Reconstitute dried conjugate 100x concentrate with 0.3 ml of deionised or distilled water. Mix gently to ensure 
complete solubilisation. Working strength conjugate is prepared by diluting the required amount of reconstituted 
conjugate 100x concentrate in green diluent as set out in the package insert. Working strength conjugate should 
be used within six hours of preparation. 

Prior to assay, mix plasmas thoroughly. 

Add 50 µl of freshly prepared working strength conjugate to each ELISA well. 

Add 50 µl of test plasma samples to appropriate wells. Add 50 µl each of the standards 1 to 4. The standards 
should be assayed at least in duplicate (triplicate preferred). 

Mix the conjugate and plasma samples/standards thoroughly using a microplate shaker for one minute at 500 to 
1 000 rpm. 

Cover each plate and incubate at room temperature (22°C ± 5°C) for 120 ± 5 minutes. Plates should not be 
exposed to direct sunlight during incubation. Deviation from specified temperature range can lead to erroneous 
results. 

During incubation, dilute one part wash buffer 20x concentrate with 19 parts deionised or distilled water and mix 
thoroughly. Wash wells with 400 µl of working strength wash buffer. Perform the wash step at least six times. An 
automated plate washer is recommended for safety reasons when handling plasma samples. 

Thorough washing is very important to the performance of the assay. When an automated plate washer is used, 
standard laboratory disinfectant should be added to the effluent reservoir, and established decontamination 
procedures for potentially infectious material should be followed. 

Tap the plates face down on absorbent towel to remove residual wash buffer. Add 100 µl of enzyme substrate 
solution to each well and mix for one minute at 500 to 1 000 rpm using a microplate shaker. 

Cover each plate with a lid and incubate at room temperature (22°C ± 5°C) for 30 minutes. Plates should not be 
exposed to direct sunlight during incubation. 

Following the 30-minute incubation, add 50 µl of enzyme-stopping solution to each well and mix thoroughly. 
Enzyme-stopping solution should be added to wells in the same order and at approximately the same speed as the 
substrate in step 11. 

Measure the optical density (OD) of each well within five minutes of stopping the reaction using a microplate 
reader fitted with a 450 nm filter and with a 620 nm to 650 nm reference filter. OD values are used to calculate 
results. 

28 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Report interpretation 
The predictive value of QFT-G results depends on the prevalence of M. tuberculosis infection in the tested 
population. Each QFT-G result and its interpretation should be considered in conjunction with other 
epidemiological, historical, physical, and diagnostic findings. The magnitude of the measured IFN-γ level cannot be 
correlated to stage or degree of infection, level of immune responsiveness, or likelihood for progression to active 
disease. Actual test data should not be reported. QuantiFERON-TB Gold IT results are interpreted using the 
following criteria (Tables 5–6). 

Table 5. QuantiFERON-TB Gold results interpretation 

TB antigen minus Nil (IU/ml)  Nil (IU/ml) 

<0.35 or  
≥0.35 and <25% of Nil value 
≥0.35 and ≥ 25% of Nil value 

<0.35 or 
≥0.35 and <25% of Nil value 

≤8.0 

≤8.0 

≤8.0 

Mitogen 
minus Nil 
(IU/ml) 

≥0.5 

Any 

Positive 

<0.5 

Indeterminate 

QuantiFERON-TB 
Gold IT Result 

Report/interpretation 

Negative 

MTB infection NOT likely 

MTB infection likely 
Results cannot be 
interpreted as a result of 
low mitogen response 
Results cannot be 
interpreted as a result of 
high background response 

Any 

>8.0 

Any 

Indeterminate 

Table 6. QuantiFERON-TB Gold PLUS results interpretation 

Nil 
(IU/ml) 

TB1 minus Nil or 
TB2 minus Nil (IU/ml) 

≤8.0 

≤8.0 

≥0.35 and ≥ 25% of Nil 

<0.35 

≤8.0 

≥0.35 and <25% of Nil 

Mitogen 
minus Nil 
(IU/ml)* 
Any 

≥0.5 

≥0.5 

QFT-Plus 
Result 

Positive 

Negative 

Negative 

≤8.0 

<0.35 

<0.5 

Indeterminate 

≤8.0 

≥0.35 and <25% of Nil 

<0.5 

Indeterminate 

>8.0 

Any 

Any 

Indeterminate 

Report/interpretation 

M.tuberculosis infection likely 
M. tuberculosis infection 
NOT likely 
M. tuberculosis infection 
NOT likely 
Results are indeterminate for TB-
antigen responsiveness 
Results are indeterminate for TB-
antigen responsiveness 
Results are indeterminate for TB-
antigen responsiveness 

Limitations 
 
 

 

Diagnosis of LTBI means tuberculosis disease must be excluded by medical evaluation. 
A negative result must be considered in conjunction with the individual’s medical and historical data, 
particularly for individuals with impaired immune function. 
There are technical factors related to indeterminate results: 
 
 

Longer than 16 hours from blood drawing to incubation at 37°C ± 1°C 
Storage of filled blood collection tubes outside the recommended temperature range (22°C ± 5°C) 
prior to 37°C ± 1°C incubation 
Insufficient mixing of blood collection tubes; and 
Incomplete washing of the ELISA plate. 

 
 

If technical issues are suspected with the collection or handling of blood samples, the entire QuantiFERON-TB Gold 
IT test should be repeated. Please note that responses to the mitogen positive control (and occasionally TB 
antigen) can be outside the range of the microplate reader. This has no impact on test results. 

Quality control 

Internal quality assessment (IQA) 
Test accuracy depends on the generation of an accurate standard curve. Results derived from the standards must 
be examined before test sample results can be interpreted. Each laboratory should determine appropriate types of 
control materials and frequency of testing in accordance with local, regional, national, or other applicable 
accrediting organisations (e.g. positivity rate, indeterminate rate). 

29 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Quality control parameters 
 
 
 
 

The mean OD value for standard 1 must be ≥ 0.600. 
The mean OD value for the zero standard (green diluent) should be≤ 0.150. 
The % coefficient of variation (% CV) between replicates for standards 1 and 2 must be ≤15%. 
Replicate OD values for standards 3 and 4 must not vary by more than 0.040 optical density units from their 
mean. 
The correlation coefficient (r) calculated from the mean absorbance values of the standards must be 
≥ 0.98. 
If the above criteria are not met, the run is invalid and must be repeated. 

 

 

External quality assessment (EQA) 
Extensive quality management, including both internal and external quality assurance, is a keystone of TB 
laboratory diagnosis and is essential for the laboratory accreditation. The UK National External Quality Assessment 
Service (UK NEQAS, www.ukneqas.org.uk) has recently established an EQA scheme for QuantiFERON-TB Gold 
tests, which is also available for customers outside the UK. Qiagen offers the QFT-G test panel (Cat No 0594-0805), 
comprising three sets of interferon-gamma (IFN-γ) controls made up of recombinant human IFN-γ. Each complete 
set consists of three individual controls representing different IFN-γ concentration levels (levels 1, 2, and 3) within 
the linear range of QuantiFERON assays. New schemes are being developed based on previous experience [15,16] 
and should be established as soon as possible. 

3.3.6 Procedure 2: T-SPOT procedure2 

General principles 
T-SPOT (Oxford Immunotec, Abingdon, UK), unlike QuantiFERON-TB Gold, uses an enzyme-linked immunospot 
(ELISPOT) technique based on enumeration of activated specific T-cells responding to stimulation by specific 
antigens (ESAT-6 and CFP10) and resulting in IFN-γ secretion. Stimulation by ESAT-6 and CFP10 antigens takes 
place in separate microtitre plate wells. 

During the course of the procedure, peripheral blood mononuclear cells (PBMCs) are separated from a whole blood 
sample and counted so that a standardised cell number is used in the assay. The PBMCs are incubated with the 
antigens to allow stimulation of any sensitised T-cells present; secreted IFN-γ is captured by specific antibodies on 
the membrane at the base of the well. A second antibody, conjugated to alkaline phosphatase and directed to a 
different epitope on the (cytokine) IFN-γ molecule, is then added and binds to the cytokine captured on the 
membrane surface. Finally, a soluble substrate is added to each well; this is cleaved by bound enzyme to form a 
spot of insoluble precipitate at the site of the reaction. Each spot therefore represents the footprint of an individual 
cytokine-secreting T-cell, and evaluating the number of spots obtained provides a measurement of the abundance 
of M. tuberculosis-sensitive effector T-cells in the peripheral blood. 

Baseline epidemiological data 
As for the QuantiFERON-TB Gold assay, baseline epidemiological data are necessary for the correct clinical 
interpretation of the test results. Data should include name and surname, full address, contact information, gender, 
occupation, place of birth, time since immigration (if applicable), travel history, history of BCG vaccination and TST, 
relevant clinical data (medication uptake, immunosuppression, weight loss, night sweats, fever, cough, abnormal 
CXR, previous TB treatment/chemoprophylaxis, etc.). Baseline data should be recorded on the patient data sheet 
that accompanies the specimen (see Chapter 3, Appendix 1). 

Safety 
This diagnostic procedure involves the handling of human blood samples and plasma, potentially infected with 
blood-borne infections, including HIV, hepatitis B, and hepatitis C. Protective equipment (gloves, lab coats and 
goggles or shields) should be worn when handling blood/plasma specimens. Handling, storage and disposal of 
blood specimens should be in accordance with national, state or local biohazard and safety guidelines or 
regulations. Risk assessment should be performed prior to introduction of the procedures and standard operating 
procedures should be developed and regularly updated. 

2 Descriptions of laboratory procedures are based on the manufacturer’s recommendations (Oxford Immunotec) and international 
safety, quality control and laboratory management regulations. 
Oxford Immunotec T-SPOT.TB96 package insert available from: http://www.oxfordimmunotec.com/96-UK 

30 

 
 
 
 
 
 
                                                                    
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Important notes: 

 

 

 

T-SPOT assay involves human PMBC cultivation. Therefore, it is extremely important to use an aseptic 
technique in order to avoid contamination of reagents, wells, cell cultures, and nourishing media; 
Blood should be progressed into the assay within eight hours of collection. This time can be prolonged by 
using the T-cell Xtend reagent (also available from Oxford Immunotec). In this case the sample storage 
time before assay is increased to 32 hours. Only lithium-heparine tubes can be used in conjunction with T-
cell Xtend;  
Calculations for the conjugate dilution, cell counting, etc. are provided on the CD-ROM supplied along with 
the kits. 

Materials 
Provided by the manufacturer with the kits (Table 7): 

Table 7. Materials provided by the manufacturer 

T-SPOT TB 96 kit 

T-SPOT TB 8 kit 

1 

2 

3 

4 

5 

6 

One microtitre plate: 96 wells coated with a mouse 
monoclonal antibody to IFN-γ. 

One microtitre plate: 96 wells, supplied as 12x8-well 
strips in a frame, coated with a mouse monoclonal 
antibody to IFN-γ 

Two vials (0.7 ml each) Panel A: contains ESAT-6 
antigens 

Two vials (0.8 ml each) Panel A: contains ESAT-6 
antigens 

Two vials (0.7 ml each) Panel B: contains CFP10 
antigens 

Two vials (0.8 ml each) Panel B: contains CFP10 antigens 

Two vials (0.7 ml each) Positive control: contains 
phytohaemagglutinin (PHA) 

Two vials (0.8 ml each) Positive control: contains 
phytohaemagglutinin (PHA) 

One vial (50 µl) 200x concentrated conjugate 
reagent: mouse monoclonal antibody to IFN-γ 
conjugated to alkaline phosphatise. 

One vial (50 µl) 200x concentrated conjugate reagent: 
mouse monoclonal antibody to IFN-γ conjugated to 
alkaline phosphatase 

One bottle (25 ml) substrate solution: ready to use 
BCIP/NBT (plus) solution. 

One bottle (25 ml) substrate solution: ready to use 
BCIP/NBT (plus) solution. 

All reagents except the conjugate are supplied ready to use. The conjugate should be diluted with PBS 1:200 
immediately prior to use (50 µl working strength solution per well). 

Equipment and materials required but not provided with the kits: 

 
 

 
 
 
 
 
 

Class II microbiological cabinet (recommended to observe aseptic technique) 
Centrifuge for preparation of PBMCs (capable of at least 1800xg and able to maintain the samples at room 
temperature (18–25°C) 
Haemocytometer 
Inverted microscope (e.g. Wilovert S, Wetzlar, Germany) 
A humidified incubator capable of 37 ± 1°C with a 5% CO2 supply 
A microtitre plate washer or equipment to manually wash plates (e.g. multichannel pipette) 
Pipettes and sterile pipette tips 
Instruments for the plate reading: Microscope, or digital microscope, or magnifying glass, or plate imager 
(e.g. ELR02, Autoimmun Diagnostika GmbH, Germany). 

Consumables: 

 
 

Sterile pipette tips 
Blood collection tubes with heparin or sodium citrate (such as Vacutainer CPT). EDTA tubes are NOT 
recommended. 

Reagents: 

 
 
 

 
 

 

Ficoll-Paque* PLUS or alternative PBMC separation materials 
Trypan blue dye (available from Sigma, catalogue number T8154) 
Sterile PBS solution, available from Invitrogen as ‘GIBCO Dulbecco's Phosphate-Buffered Saline (D-PBS) 
(1x)’, catalogue number 14040-091). Do not use PBS containing Tween 
Distilled or deionised water 
Sterile serum-free cell culture medium such as ‘GIBCO AIM V’ (Invitrogen; catalogue number 31035-025) 
(for incubation) 
Sterile cell culture medium RPMI 1640 (Invitrogen; catalogue number 21875-034) (for initial cell preparation 
and cell suspension dilution). 

31 

 
 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Sample collection 

Blood should be collected as follows: 

 
 
 

Adults and children 10 years old and over: one 8 ml or two 4 ml CPT tubes or one 6 ml lithium heparin tube 
Children 2–9 years old: one 4 ml CPT or lithium heparin tube 
Children up to 2 years old: one 2 ml paediatric tube. 

After collection, blood should be stored at room temperature (no refrigeration or freezing) and assayed within eight 
hours. This time period can be prolonged to 32 hours if T-Cell Xtend is used. The T-Cell Xtend reagent should be 
added prior to PBMC separation using standard separation techniques. Whole blood samples should be stored at 
room temperature (18–25°C) between 23 and 30 hours post venipuncture with the use of T-Cell Xtend reagent.  

If the T-Cell Xtend reagent is to be used, immediately before cell separation remove the cap from the blood 
collection tube and add 25 µl of the T-Cell Xtend reagent solution per ml of blood sample.  

Replace the cap and invert the blood collection tube gently eight to ten times to mix. Incubate for 20 ± 5 minutes 
at room temperature (18–25°C) and then proceed to isolate the PBMC layer using Ficoll density gradient 
centrifugation. 

Sample preparation 

Initial sample preparation steps depend on whether Vacutainer CPT or conventional Lithium-heparin or sodium 
citrate tubes were used for the blood collection. Please note that T-Cell Xtend reagent is NOT compatible with the 
CPT tubes. Leucosep tubes are now validated for use with the T-SPOT.TB assay, and can be used with T-Cell Xtend 
simplifying Ficoll preparation of peripheral blood mononuclear cells (PBMCs). The Leucosep tube eliminates the 
time-consuming and laborious layering of the sample material over FICOLL-PAQUE PLUS. For details of the 
specimen preparation procedures involving T-Cell Xtend, please refer to the T-SPOT TB Technical handbook 
available at http://www.oxfordimmunotec.com/UK%20Technical%20Handbook. 

CPT tubes (with gel plug) 

 

 

Centrifuge 8 ml CPT tubes at 1600xg for 28 minutes or 4 ml CPT tubes at 1800xg for 30 minutes at 18°C if 
a refrigerated centrifuge is available. If a non-refrigerated centrifuge is used, ensure the temperature does 
not go above 25°C; 
Collect the white, cloudy band of PBMCs using a pipette and transfer to a 15 ml conical centrifuge tube. 
Make up the volume to 10 ml with cell culture medium AIM V or RPMI 1640. 

Lithium-heparin/sodium citrate tubes 

 

 

 

 
 

Dilute the blood with an equal volume of RPMI 1640 medium. Carefully layer the diluted blood (2–3 
volumes) onto Ficoll-Paque PLUS (1 volume) and centrifuge at 1000xg for 22 minutes while maintaining the 
temperature between 18 and 25°C. 
Collect the white, cloudy band of PBMCs using a pipette and transfer to a 15 ml conical centrifuge tube. 
Make up the volume to 10 ml with cell culture medium AIM V or RPMI 1640. 
Centrifuge at 600xg for seven minutes. Pour off the supernatant and re-suspend the pellet in 1 ml AIM V or 
RPMI medium. 
Make up the volume to 10 ml with fresh AIM V or RPMI medium and centrifuge at 350g for seven minutes. 
Pour off the supernatant and resuspend the pellet in 0.7 ml AIM V culture medium. 

Cell counting and dilution 

The T-SPOT.TB assay requires 2.5 x 105 viable PBMCs per well. A total of four wells are required for each patient 
sample. The correct number of cells must be added to each well. Failure to do so may lead to an incorrect 
interpretation of the result. Care should be taken to ensure that the cell suspension is thoroughly mixed 
immediately prior to removal of aliquots for dilution or for counting. 

For manual counting with a Neubauer haemocytometer, add 10 µl of the final cell suspension to 40 µl 0.4% (w/v) 
trypan blue solution. Place an appropriate aliquot onto the haemocytometer and count the cells in the grid. For 
other types of haemocytometers and for automated devices, follow the manufacturer’s instructions. 

Calculate the concentration of viable cells present in the stock cell suspension. The T-SPOT cell dilution calculator 
on the CD-ROM provided with each assay kit will facilitate this calculation. 

Prepare 500 µl of the final cell suspension at a concentration of 2.5x105 cells/100 µl. Ensure cells are thoroughly 
mixed before removing an aliquot for dilution. 

32 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Plate set up and incubation 

The T-SPOT.TB assay requires four wells to be used for each patient sample. A nil control and a cell functionality 
positive control should be run with each individual sample. It is recommended that the samples are arranged 
vertically on the plate as illustrated below: 

 Nil control 
 Panel A 
 Panel B 
 Positive control 

 

 

 

 

Remove the pre-coated microtitre plate from the packaging and allow to equilibrate to room temperature. 
The microtitre plate is provided with a protective plastic base. This should not be removed at any stage of 
the procedure. 
Each patient sample requires the use of four individual wells as follows. (Do not allow the pipette tip to 
touch the membrane. Indentations in the membrane caused by pipette tips may cause artefacts in the 
wells). 
 
 
 
 

Add 50 µl AIM V culture medium to each nil control well. 
Add 50 µl Panel A solution to each well required. 
Add 50 µl Panel B solution to each well required. 
Add 50 µl positive control solution to each positive control well. 

To each of the four wells to be used for a patient sample, add 100 µl of the patient’s final cell suspension 
(containing 250 000 viable cells). 
Incubate the plate in a humidified incubator at 37°C with 5% CO2 for 16 to 20 hours. 

Spot development and counting 

1. 

2. 
3. 

Remove the plate from the incubator and discard the cell culture medium. Remove the substrate solution from 
the kit and allow to equilibrate to room temperature. 
Add 200 µl PBS solution to each well. 
Discard the PBS solution. Repeat the well washing a further three times with fresh PBS solution for each wash. 
Discard all PBS from the final wash step by inverting the plate on absorbent paper before proceeding. 
Dilute the concentrated conjugate reagent 1:200 in PBS to create the working strength solution. 
Add 50 µl working strength conjugate reagent solution to each well and incubate at 2–8°C for one hour. 
Discard the conjugate and perform four PBS washes as described in steps 2 and 3 above. 
Add 50 µl substrate solution to each well and incubate at room temperature for seven minutes. 

4. 
5. 
6. 
7. 
8.  Wash the plate thoroughly with distilled or deionised water to stop the detection reaction. Allow the plate to 
dry by standing it in a well-ventilated area or in an oven at up to 37°C (spots become more visible as the plate 
dries). Allow four hours drying time at 37°C or overnight at room temperature. 
Count and record the number of distinct, dark blue spots on the membrane of each well. Use a magnifying 
glass, a suitable microscope, or an ELISPOT plate reader. 

9. 

10.  Apply the results interpretation and assay criteria (see below) to determine whether a patient sample is ‘positive’ 

or ‘negative’ to TB antigens. 

Reading and results interpretation 

T-SPOT.TB results are interpreted by subtracting the spot count in the nil control well from the spot count in each 
of the panels, according to the following algorithm: 

 

 

 

The test result is ‘positive’ if (Panel A minus nil control) and/or (Panel B minus nil control) ≥ 6 spots, AND a 
nil control count <10 spots;  
The test result is ‘negative’ if both (Panel A minus nil control) and (Panel B minus nil control) ≤ 5 spots (this 
includes values less than zero), AND a nil control count <10 spots AND a positive control count >20 spots 
(or show saturation); 
The test result is ‘indeterminate’ if: 
 

a nil control count >10 spots regardless of spot counts in Panel A and Panel B; or 

33 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 

a positive control count <20 spots if both (Panel A minus nil control) and (Panel B minus nil control) 
≤ 5 spots. 

Due to potential biological and systematic variations, where the highest of Panel A minus nil control and Panel B 
minus nil control is 5, 6 or 7 spots, the result may be considered as borderline (equivocal). Borderline (equivocal) 
results, although valid, are less reliable than results where the spot count is further from the cut-off. Retesting of 
the patient, using a new sample, is therefore recommended. If the result is still borderline (equivocal) on retesting, 
then other diagnostic tests and/or epidemiological information should be used to help determine TB infection status 
of the patient. 

Reporting 
The manufacturer recommends using the following wording in the laboratory reports: 

 
 

A ‘positive’ result indicates that the sample contains effector T-cells reactive to M. tuberculosis. 
A ‘negative’ result indicates that the sample probably does not contain effector T-cells reactive to M. 
tuberculosis 

Quality control 

Internal quality assessment (IQA) 

Appropriate means of internal quality assurance and control should be determined, developed and implemented by 
each laboratory in accordance with local and governmental regulations. This can include: 

 
 
 

blind re-testing of specimens on a regular basis; 
keeping records on dates when kits are opened and finished, kit lot numbers; 
fridge and freezer temperature sheets. 

External quality assessment (EQA) 
Currently no formal EQA schemes exist for T-SPOT TB tests. These should be established and implemented as soon 
as possible based on previous experience. 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

10. 

11. 

12. 

Tufariello JM, Chan J, Flynn JL. Latent tuberculosis: mechanisms of host and bacillus that contribute to 
persistent infection. Lancet Infect Dis. 2003 Sep;3(9):578-90. 

Dye C, Scheele S, Dolin P, Pathania V, Raviglione MC. Consensus statement. Global burden of tuberculosis: 
estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project. 
JAMA. 1999 Aug 18;282(7):677-86. 

Styblo K. The relationship between the risk of tuberculosis infection and the risk of developing infectious 
tuberculosis. Bull Int Union Tuber. 1985;60:117-9. 

Flynn JL, Chan J. Immunology of tuberculosis. Annu Rev Immunol. 2001;19(1):93-129. 

World Health Organization; Stop TB Partnership. The Stop TB Strategy. Geneva: World Health Organization; 
2006. Available from: http://whqlibdoc.who.int/hq/2006/WHO_HTM_STB_2006.368_eng.pdf. 

Lee E, Holzman RS. Evolution and current use of the tuberculin test. Clin Infect Dis. 2002 Feb 1;34(3):365-70. 

Harboe M, Oettinger T, Wiker HG, Rosenkrands I, Andersen P. Evidence for occurrence of the ESAT-6 protein 
in Mycobacterium tuberculosis and virulent Mycobacterium bovis and for its absence in Mycobacterium bovis 
BCG. Infect Immun. 1996 Jan;64(1):16-22. 

Behr MA. Comparative genomics of BCG vaccines. Tuberculosis (Edinb). 2001;81(1-2):165-8. 

Andersen P, Munk ME, Pollock JM, Doherty TM. Specific immune-based diagnosis of tuberculosis. Lancet. 
2000 Sep 23;356(9235):1099-104. 

Andersen P, Doherty TM, Pai M, Weldingh K. The prognosis of latent tuberculosis: can disease be predicted? 
Trends Mol Med. 2007 May;13(5):175-82. 

Pai M. Guidelines on IGRAs: Concordant or discordant? 2nd Global Symposium on IGRAs, May 30–June 1, 
2009. Dubrovnik, Croatia. 

Nyendak MR, Lewinsohn DA, Lewinsohn DM. New diagnostic methods for tuberculosis. Curr Opin Infect Dis. 
2009 Apr;22(2):174-82. 

13.  Mazurek GH, Jereb J, Lobue P, Iademarco MF, Metchock B, Vernon A. Guidelines for using the QuantiFERON-

TB Gold test for detecting Mycobacterium tuberculosis infection, United States. MMWR Recomm Rep. 2005 
Dec 16;54(RR-15):49-55. Erratum in: MMWR Morb Mortal Wkly Rep. 2005 Dec 23;54(50):1288. 

34 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

14. 

National Collaborating Centre for Clinical Conditions. Royal College of Physicians. Tuberculosis: clinical 
diagnosis and management of tuberculosis, and measures for its prevention and control. London: Royal 
College of Physicians; 2006. Available from: http://www.nice.org.uk/nicemedia/live/10980/30020/30020.pdf. 

15.  Westgard JO, Barry PL, Hunt MR, Groth T. A multi-rule Shewhart chart for quality control in clinical 

chemistry. Clin Chem. 1981 Mar;27(3):493-501. 

16. 

17. 

18. 

19. 

20. 

Hang NT, Ishizuka N, Keicho N, Hong LT, Tam DB, Thu VT, et al. Quality assessment of an interferon-gamma 
release assay for tuberculosis infection in a resource-limited setting. BMC Infect Dis. 2009 May 18;9:66. 

Kaufmann SH. How can immunology contribute to the control of tuberculosis? Nat Rev Immunol. 2001 
Oct;1(1):20-30. 

Denkinger CM, Dheda K, Pai M. Guidelines on interferon-γ release assays for tuberculosis infection: 
concordance, discordance or confusion? Clin Microbiol Infect. 2011 Jun;17(6):806-14 

Pai M, Denkinger CM, Kik SV, Rangaka MX, Zwerling A, Oxlade O, et al. Gamma interferon release assays for 
detection of Mycobacterium tuberculosis infection. Clin Microbiol Rev. 2014 Jan;27(1):3-20 

European Center for Disease Prevention and Control. Use of interferon-gamma release assays in support of 
TB diagnosis. Stockholm. 2011. Available from: http://ecdc.europa.eu/en/publications/Publications/ 
1103_GUI_IGRA.pdf. 

21.  World Health Organization. Guidelines for intensified tuberculosis case-finding and isoniazid preventive 

therapy for people living with HIV in resource-constrained settings. Geneva, 2011. Available from: 
http://whqlibdoc.who.int/publications/2011/9789241500708_eng.pdf. 

22.  World Health Organization. Use of tuberculosis interferon-gamma release assays (IGRAs) in low-and middle-
income countries: policy statement. Available from: http://www.who.int/tb/features_archive/policy_ 
statement_igra_oct2011.pdf. 

23.  World Health Organization. Guidelines on the management of latent tuberculosis infection. Available from: 

http://apps.who.int/iris/bitstream/10665/136471/1/9789241548908_eng.pdf. 

24. 

Rangaka MX, Wilkinson KA, Glynn JR, Ling D, Menzies D, Mwansa-Kambafwile J.. Predictive value of 
interferon-gamma release assays for incident active tuberculosis: a systematic review and meta-analysis. 
Lancet Infect. Dis. 2012;12:45–55 

25.  Machingaidze S, Verver S, Mulenga H, Abrahams DA, Hatherill M, Hanekom W, et al. Predictive value of 

recent QuantiFERON conversion for tuberculosis disease in adolescents. Am. J. Respir. Crit. Care Med. 
2012;186:1051–1056. 

26. 

27. 

Kim YJ, Kim SI, Kim YR, Wie SH, Park YJ, Kang MW.. Predictive value of interferon-gamma ELISPOT assay in 
HIV 1-infected patients in an intermediate tuberculosis-endemic area. AIDS Res. Hum. Retroviruses 2012; 
28:1038–1043 

Cattamanchi A, Smith R, Steingart KR, Metcalfe JZ, Date A, Coleman C, Marston BJ, Huang L, Hopewell PC, 
Pai M. Interferongamma release assays for the diagnosis of latent tuberculosis infection in HIV-infected 
individuals—a systematic review and meta-analysis. J. Acquir. Immune Defic. Syndr. 2011;56:230–238 

28. 

Diel R, Loddenkemper R, Nienhaus A. Predictive value of interferon-gamma release assays and tuberculin skin 
testing for progression from latent TB infection to disease state: a meta-analysis. Chest 2012;142:63–75. 

35 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Appendix: Patient data sheet 

Sender’s contact details: 
Name 
Laboratory/hospital 
Postal address 
Phone 
Fax 

For laboratory use 
Patient’s number  
Date received  
Time received  
Date of test  

Please circle/mark/tick appropriate answer(s). Please do not leave any fields blank. 
If answer requires further details, please specify. 
Please remember that complete answers are essential for the correct interpretation of the test results. 

Baseline epidemiological data 
Patient’s first name 
Surname 
Date of birth 
Male ___ Female ___ 
Postcode 
Occupation 
Was the patient born abroad? 
Yes 
No 
If no, when did the patient come to __________________________________ (country)? _________ (year) 
Has patient lived, or spent more than two months travelling in another country? 
Yes ___ 
No ___ 
Don’t know 

___ 
___ Born in ________________ 

History of BCG vaccination and TB skin tests 

Has patient ever received a BCG vaccination? Yes ___ No ___ Don’t know ___ 

If yes, please specify age: ___ 
BCG scar: Yes ___ No ___ 

TB skin test done? Yes ___ No ___ Don’t know ___Reading ____ mm 

Clinical data 
Is patient taking any of the following medications?  
___ Oral steroids 
___ Cytotoxic drugs 
___ Other immunosuppressive drugs (please specify) 
___ None of the above. 
Is the patient immunocompromised? Yes ___ No ___ Don’t know ___ 
Is the patient HIV positive? Yes ___ No ___ Don’t know ___ 
Does the patient have diabetes? Yes ___ No ___ Don’t know ___ 
Does the patient have any of the following:  
___ Fever  
___ Night sweats  
___ Loss of weight  
___ Cough  
Is the patient’s CXR abnormal? Yes ___ No ___. If yes, please specify the location:  

Cavities? Yes ___ No ___ Don’t know ___ 
Consolidation? Yes ___ No ___ Don’t know ___. Unilateral/bilateral?  
Other relevant clinical data: 

36 

RLowerMiddleUpperL 
 
 
 
 
 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

4. Smear microscopy 

Susana David, Vera Katalinić-Janković, Daniela Cirillo 

Revised by Emanuele Borroni and Enrico Tortoli, 2015 

4.1 Background and principles 

Early laboratory diagnosis of tuberculosis still relies on the examination of stained smears. For universal application 
in resource-limited countries, microscopy of stained sputum smears is the best choice among diagnostic methods 7, 
12]. This technique is based on the fact that the cell wall of the Mycobacterium spp. genus is rich in complex lipids 
that prevent access to common aniline dyes, but when stained with carbol-fuchsin or fluorochromes under special 
staining conditions, these are not easily decolourised, even with alcohol-acid solutions. Because of this 
characteristic, all members of Mycobacterium spp., not only M. tuberculosis, are referred to as acid-fast bacilli 
(AFB). 

At present, two types of acid fast stains are used to detect mycobacteria in clinical specimens: 

 

 

Carbol-fuchsin staining (Ziehl-Neelsen [ZN] method and its modification performed without heating the dye 
[Kinyoun cold staining]); and 
Fluorochrome (auramine or auramine-rhodamine) staining. 

Kinyoun staining is a modification of the classic ZN staining which excludes the heating step during the staining 
procedure and uses a higher concentration of carbol-fuchsin. Mycobacteria appropriately stained by ZN and Kinyoun 
appear as red rods. Kinyoun staining is not as effective as ZN, therefore this procedure is not recommended [6]. 

Methods which apply a fluorochrome have been used to stain acid fast bacteria for many years. Using this method, 
mycobacteria are detected as bright fluorescent rods against a darker background. Fluorochrome staining has an 
increased sensitivity and less time is required to screen the slides when compared to Kinyoun or ZN staining because 
slides are screened at lower magnification [6]. 

Smear microscopy is simple, inexpensive and efficient in detecting those cases of pulmonary tuberculosis that are most 
infectious. Since its yield is highly dependent on its execution, the quality of smear microscopy is crucial in the fight 
against TB in resource-limited settings [6,7]. 

A major limitation of smear microscopy is its low sensitivity (25–75% compared to culture) and the high number of bacilli 
required for positivity (in the range of 5 x 103–104 bacilli per ml). Sensitivity and the positive predictive value (PPV) of 
smear microscopy are influenced by numerous factors [7,12,13] such as the prevalence and severity of the disease, the 
type and quality of the specimen, the number of mycobacteria in the sample and the quality of the smear preparation, 
staining and reading process. Smear microscopy does not allow for mycobacterial species identification, nor does it give 
an indication of the viability of mycobacteria in the sample. HIV co-infected TB patients may have disseminated 
paucibacillary disease with fewer AFB. Smear microscopy is often negative or may require more scrutiny in screening to 
identify lower numbers of AFB. 

4.2 Procedure 1: Ziehl-Neelsen (ZN) 

Each batch of prepared reagent should be recorded in a reagent preparation workbook which includes: the 
signature of the technician who prepared it, the date of preparation and the results of quality control testing [2,6]. 

4.2.1 Ziehl-Neelsen (ZN) reagent preparation 

Good staining reagents, made with high-quality carbol-fuchsin dye are essential for detecting AFBs [6]. 
Contamination of reagents by environmental mycobacteria should be prevented by using freshly distilled water. 

Standard reagents: 

 
 
 
 

Basic fuchsin powder 
Phenol crystals (the crystals should be almost colourless) 
Alcohol (denaturated 95% ethanol) 
Water (distilled or purified). 

Decolourising solution: 

 
 
or 
 
 

Concentrated sulphuric acid (≥95%) 
Water (distilled or purified) 

Hydrochloric acid (37%) 
Alcohol (denaturated 95% ethanol). 

37 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

The counterstain solution: 

 
 

Methylene blue powder 
Water (distilled or purified). 

A. Carbol-fuchsin (CF) reagent 
The quality of basic fuchsin varies among different manufacturers with regard to its purity and solubility. The basic 
fuchsin content should represent 85–88% of the weight. If carbol-fuchsin purity is known, it should be used to calculate 
the final stain concentration of 0.3%. To calculate the required amount of basic fuchsin, divide the actual amount by the 
dye content. For instance, if the dye content is 75%, you must divide the amounts by 0.75. So 3 g/0.75 = 4 grams will 
be weighed for the 0.3% stain. If powder with a dye content of >85% is used, there is no need to calculate the 
correction factor. If the dye purity is unknown or if the basic fuchsin dissolves poorly or precipitates are still visible after 
filtration, it may be wise to use the higher concentration (1%) when preparing the staining reagent. 

0.3% Carbol-fuchsin 

Basic fuchsin 
95% ethanol 
Phenol crystals 
Distilled water 

3.0 g 
100 ml 
50 g 
900 ml 

 
 
 
 

Weigh 3.0 g of basic fuchsin powder and 50 g of phenol crystals separately. 
Add 100 ml of alcohol (denatured ethanol) to a 1-l conical flask. 
Add 50 g of phenol and swirl the flask until it is dissolved. 
Add 3.0 g of basic fuchsin powder and continue to mix well until the fuchsin powder completely dissolves.  

Check for remaining powder or crystals on the bottom. If there are any, continue swirling with slight heating. Only 
after the fuchsin is completely dissolved, add 850 ml of water and mix by continuing to swirl. 

If precipitates are visible, the carbol-fuchsin staining reagent should be filtered. Filter the carbol-fuchsin again 
during the staining process, using a funnel with filter paper (or by placing a piece of filter paper directly on the 
slide). Other staining reagents do not need to be filtered. If any particles are detected in the carbol-fuchsin 
solution, the solution must be refiltered. 

B. Decolourising solution 

25% sulphuric acid 

Concentrated sulphuric acid 
Distilled water 

250 ml 
750 ml 

 
 
 

 

Add 750 ml of distilled water to a 2-l conical flask. 
Measure 250 ml of concentrated sulphuric acid in a cylinder. 
Pour it slowly into the flask containing the water, directing the flow of acid gently along the inner side of the 
flask. Always add the acid slowly to the water, not vice versa. 
Mix well by swirling the flask. 

3% HCl ethanol 

Concentrated hydrochloric acid 
95% ethanol 

30 ml 
970 ml 

 
 
 

 

Add 970 ml of 95% ethanol to a 2-l conical flask. 
Measure 30 ml of concentrated hydrochloric acid into a cylinder. 
Pour it slowly into the flask containing alcohol, directing the flow of acid gently along the inner side of the 
flask with constant swirling. Always add the acid slowly to the alcohol, not vice versa. 
Mix well by swirling. 

C. Counterstain 

Methylene blue chloride 

Distilled water 

3.0 g 

1000 ml 

Weigh 3 g of methylene blue powder. 
Add the powder to 0.5 l of pure water in a conical flask. 
Swirl the contents of the flask to dissolve the dye. 
Add 0.5 l of water and mix again. 

 
 
 
 

38 

 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

4.2.2 Storage of reagents 

The flasks of freshly-prepared reagents should be covered until quality control procedures have been performed 
and the results have been evaluated [7]. Solutions should be stored in clean brown bottles and clearly labelled. The 
label should indicate the reagent name, concentration and the preparation date. Reagents preserved in tightly 
closed bottles can be used for up to one year. Bottles should be kept out of direct sunlight. If clear bottles are 
used, stocks of reagents should be stored in a closed cabinet. 

4.2.3 Quality control of freshly-prepared staining reagents 

After preparing staining reagents, quality control checks should be performed on every batch [7,14]. Quality control 
is essential to ensure the effectiveness of staining reagents and the complete absence of AFB contamination. 

Quality control results should be recorded in a logbook, with every batch clearly identified by the name of the 
reagent and the preparation date on the bottle labels. Perform quality control by using one or more freshly-
prepared staining reagents, carrying out the usual staining procedure as described for positive controls. Test the 
performance of cabol-fuchsin by staining and examining two scanty or 1+ smears stained once, and two negative 
smears stained three times [2]. 

4.3 Procedure 2: Fluorochrome staining 

4.3.1 Quality control of freshly-prepared staining reagents 

A. Fluorochrome reagents 

Auramine O (solution 1) 

Auramine 
95% ethanol 

Phenol crystals 
Distilled water 

Phenol (solution 2) 

0.1 g 
10 ml 

3.0 g 
87 ml 

Dissolve phenol crystals in water. 

Mix solutions 1 and 2 and store in a tightly-stoppered, dark-coloured bottle away from heat and light. Label bottles 
with the name of the reagent, the date of preparation and expiry date. Store at room temperature for three 
months. When left standing turbidity may develop but this does not affect the staining reaction. 

B. Decolourising solution 

Concentrated hydrochloric acid 
70% ethanol 

0.5% Acid alcohol 

0.5 ml 
100 ml 

Carefully add concentrated hydrochloric acid to the ethanol. Always add acid slowly to the alcohol, not vice versa. 
Store in a dark-coloured bottle. Label bottles with the name of the reagent, the date of preparation and expiry 
date. Store at room temperature for three months. For each volume of stain, 2 to 3 volumes of decolourising 
solution are needed. 

C. Counterstains 
Either potassium permanganate or acridine orange may be used as counterstains. 

Potassium permanganate 

Potassium permanganate (KMnO4) 
Distilled water 

0.5 g 
100 ml 

Dissolve potassium permanganate using distilled water in a tightly-stoppered, dark-coloured bottle. Label bottles 
with the name of the reagent, the date of preparation and expiry date. Store at room temperature for up to three 
months. 

39 

 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Acridine orange 

Anhydrous dibasic sodium phosphate (Na2HPO4) 
Distilled water 
Acridine orange 

0.01 g 
100 ml 
0.01 g 

Dissolve sodium phosphate in distilled water. Add acridine orange and mix until dissolved. Store in a tightly 
stoppered dark-coloured bottle away from heat and light. Label bottles with the name of the reagent, the date of 
preparation and expiry date. Store at room temperature for three months. 

4.3.2 Safety measures 

Never add water to acid. To reduce exposure to toxic phenolic fumes, reagents and staining solution containing 
phenol should be prepared in a well-ventilated area or under a chemical hood. Always wear protective laboratory 
coats, gloves and safety glasses when handling a strong acid. In the event of an accident with acid, rinse the 
affected body part immediately with plenty of water. 

4.4 Sample collection 

Smear microscopy for Mycobacterium spp. detection can be used for a wide variety of biological samples. For the 
diagnosis of respiratory tuberculosis, sputum is the most commonly used sample. To ensure optimal recovery of TB 
bacilli from sputum, at least two specimens should be collected and processed for mycobacterial microscopy and 
culture [7,15]. 

Country guidelines will provide information on the number of recommended samples. Early morning specimens 
have the highest yield of AFB; however, it is now proven that good diagnostic specimens can be collected at any 
time. It is not recommended to perform smear microscopy from blood or very bloody samples due to the low 
sensitivity of the procedure. It is also not recommended to routinely perform smear microscopy from urine samples 
due to the frequent detection of saprophytic mycobacteria colonising the urogenital tract. 

Samples should be collected in clean, wide-mouthed and leak-proof specimen containers [2,6]. Single use 
disposable plastic containers (50 ml capacity) are preferred in order to avoid transferring the specimens from one 
container to another. Alternatively, 50 ml disposable sterile conical tubes can be used. 

Patients should receive clear written instructions on the proper collection of the sputum specimen for TB diagnosis. 
For patients on treatment, specimens should be collected at intervals specified in accordance with the country’s 
guidelines [7]. Sputum collection should never be performed in the laboratory. It is a procedure generating 
infectious aerosols and should only be performed at a distance from other people, preferably in open spaces where 
possible, or in rooms with negative pressure and adequate air exchange [7,14]. 

A good specimen should be approximately 3–5 ml in volume [5]. Sputum specimens should appear thick and 
mucoid or clear but with purulent grains [7]. The colour varies from opaque white to green. Bloody specimens will 
appear reddish or brown. Note: clear saliva or nasal discharge is not suitable as a TB specimen [2,15]. 

4.4.1 Specimen handling 

For optimum patient management, process the specimen as soon as possible (i.e. < 24 hours). For microscopic 
examination, the interval between collection and staining is not critical. Acceptable results can be obtained even if 
specimen delivery has been delayed. 

4.4.2 Criteria of acceptability 

Upon arrival in the laboratory, the quality of sputum samples should be assessed and reported in the referral form 
[7]. TB-positive sputa can vary in colour and aspect. If the sample is liquid and is clear and water-like, without 
particles or streaks of mucous material, process the sample but ensure that the poor quality of the sample is 
reported on the result form. When possible, encourage the patient/physician to submit a new specimen; however, 
even saliva can yield positive results. All specimens should be processed, except for broken or leaking containers 
which should be discarded and another specimen requested. 

Accept very small quantities if the patient has difficulty producing sputum. Blood-streaked sputum is suitable, but 
pure blood should not be examined [1,2]. 

40 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

4.5 Smear preparation 

Although smear preparation for AFB detection [7] is a relatively safe procedure in terms of infected aerosol 
production, it is recommended that the slides be prepared in a class I or IIB biological safety cabinet [14,15] if 
available. If the smear is prepared after centrifugation of the sample (concentrated smear), the centrifuge holder 
must be opened within a biological safety cabinet. 

 

 

 

 

 
 
 

 

 
 
 

 

Smears should be prepared using new, clean, grease-free and unscratched slides. Using a pencil, record the 
laboratory register serial number and order number of the specimen on the frosted end of the slide. If plain 
unfrosted slides are used, label them using a diamond pencil. 
If smear is prepared directly from a fresh sample (without prior centrifugation) use an applicator stick or 
wire/disposable loop, select and pick up the yellowish purulent particles of sputum. For re-suspended pellets 
(after the centrifugation) a disposable loop is advisable. 
Prepare the smear in an oval shape in the centre of the slide. The smear size should be 2–3 cm in length 
and 1–2 cm wide, which will allow 100–150 fields to be counted in one length. 
For good spreading of the sputum, press the stick firmly perpendicular to the slide and move in small 
concentric circles or coil-like patterns. 
Place the used stick in a discard container.  
Use a separate stick for each specimen.  
Thorough spreading of the sample is very important, especially in the case of thick or purulent material; it 
should be neither too thick nor too thin. Prior to staining, hold the smear about 4–5 cm over a piece of 
printed paper. If letters cannot be read, it is too thick. 
For concentrated samples (after centrifugation at 3000x g for 20 minutes, see sample preparation for TB 
culture) one or two drops of sediment should be smeared on the slide. 
Allow the smear to air-dry completely at room temperature within the biological safety cabinet. 
Do not dry smears in direct sunlight or over a flame. 
Pass the slide over a flame 2–3 times for about 2–3 seconds each time. Do not heat the slide for too long or 
keep it stationary over the flame or else the slide will be scorched. 
Alternatively, slides can be fixed for two hours on hot plates (65–75°C), within the biological safety cabinet. 

Table 8 lists the equipment needed for direct (unconcentrated) smear microscopy. 

Table 8. Equipment required for smear preparation and staining 

Equipment required for smear preparation and staining 

Container to store specimen 
Wire loop with an inner diameter of 3 mm to spread sputum on the slide 
Microscope slide (grease-free and unscratched) 
Marking pen to put the identification number on the microscopy slide 
Forceps to hold smear slide 
Bunsen burner to fix the smear slide and flame the smear during staining 
Staining rack to hold the smear slide 
Slide rack in which to place stained smear slide for air-drying 

4.6 Staining procedures 

4.6.1 Ziehl-Neelsen staining method 

 
 
 

 
 
 
 
 

Cover the entire surface of each heat-fixed slide with carbol-fuchsin. 
Using a Bunsen burner, gently heat the slides until vapour rises. Do not allow them to boil.  
Allow the stain to remain on the slide for ten minutes. Adequate time is required for the carbol-fuchsin to 
penetrate and stain the cell well. 
Gently wash the stain from each slide with a stream of cold water until all the free stain has washed away. 
Cover each slide with acid alcohol; wait three minutes. 
Rinse slides again carefully with water and tilt each slide to remove excess water. 
Flood the slide with the methylene blue counterstain for one minute. 
Rinse slides again carefully with water, drain and air dry. 

41 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

4.6.2 Fluorochrome staining method 

 
 
 
 
 

 
 
 
 

 
 

Prepare and heat fix smears. 
Place the numbered smears on a staining rack in batches (maximum 12). 
Flood the slides with auramine O stain and allow them to stain for 15 minutes. 
Be sure that the stain stays on the smear. Do not heat and do not use paper strips.  
Rinse the slide with water. Aim the flow of water at the edge of the slide and slowly peel the stain from the 
slide.  
Flood the slides with 0.5% acid alcohol and allow them to decolourise for three minutes. 
Ensure that the slides are flooded thoroughly with acid alcohol.  
Rinse off the 0.5% acid alcohol with water, drain the excess water from the slide. 
Flood each slide with potassium permanganate and allow it to quench for two minutes.  
Note: It is critical that the potassium permanganate remains on the slides for no longer than two minutes as 
over-quenching of fluorescence can occur. 
Wash off the potassium permanganate. Drain the excess water from the slide. 
Allow smears to air dry. Do not blot. Read as soon as possible after staining. 

4.6.3 Automatic staining 

Automated stainers that can process a large number of samples are commercially available. The machines require 
dedicated reagents and are able to perform both ZN and fluorochrome staining. Accurate and appropriate 
maintenance after each staining session is required to maintain consistent, high-quality staining. 

4.7 Microscopy 

Figure 3 shows the requirements of a microscope for smear examination. 

Figure 3. Microscope components 

Source: Lumb R, Bastian I. Laboratory diagnosis of tuberculosis by sputum microscopy. Adelaide: Institute of Medical and 
Veterinary Science; 2005. p. 38. [17] 

42 

 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

4.7.1 Maintenance 

Install the microscope on a rigid, flat, level surface, away from direct sunlight, dust, vibration (e.g. from 
centrifuges), water (sink, spray from a tap), chemical reagents or humidity.  

The modern light microscope needs no particular daily maintenance, but considerable care is required in its use. 
For further information, please refer to the microscope manual for care and maintenance information. 

4.7.2 Fluorescence microscopy 

The identification of mycobacteria with the fluorescent dye auramine O is based on the affinity of the fluorochrome 
to the mycolic acids in the cell wall. Auramine O is excited by blue light and emits in the region of ~500 nm to 
~650 nm. 

Fluorescence microscopy has some important advantages:  

 
 

 

High contrast fluorescence images allow for easier detection of AFB. 
The use of low- to medium-power lenses (typically 10x, 20x and 40x) permits a larger field of view than 
conventional microscopy, where typically a 100x lens is used. 
The fluorochrome staining method is simpler than the ZN method. 

A binocular microscope equipped with a fluorescent light source and suitable filter set is used for auramine-stained 
smears. Fluorescent light is provided by a vapour lamp (such as mercury or xenon lamps). The mercury vapour 
lamp provides the strongest light, but it has a limited lifespan of about 100 to 200 hours, which must be monitored 
with a timer. Moreover, these lamps are very expensive and fragile. 

4.7.3 Light-emitting diode (LED) microscopy 

There is a compelling base of evidence promoting ultra-bright LED microscopy as a substitute for both conventional 
fluorescence microscopy and direct ZN microscopy [11]. LED-based microscopy facilitates identification of acid-fast 
bacilli in comparison with ZN, can be used with auramine staining, is cost-effective (lifespan of the lamp is over 
10 000 hours), has low power requirements, and can be easily introduced in microscopy centres, including 
peripheral facilities. In addition, light intensity can easily be regulated. 

Since LED-based microscopy has been acknowledged as an important development in direct fluorescence 
microscopy, WHO has recommended that it replace conventional fluorescence microscopy and that it be phased in 
as an alternative to conventional ZN microscopy in both high- and low volume laboratories. During the 
implementation of LED microscopy, the following issues are of importance: training requirements, validation during 
the introductory phase, monitoring of trends in case detection and treatment outcomes. Adapted systems may 
need to be introduced for internal quality control as well as external quality assurance. 

4.8 Recording and reporting 

Recording and reporting of results [2,6,7] is summarised in Table 9. 

Table 9. Reporting of microscopy smears 

IUATLD/WHO scale 
(1000x field = HPF) 

Bright field 
(1000x magnification: 
1 length = 2 cm = 100 HPF) 

Fluorescence 
(200–250x magnification: 
1 length = 30 fields = 300 
HPF) 

Fluorescence 
(400x magnification: 
1 length = 40 fields = 200 
HPF) 

Microscopy system 

Result 

Negative 

Scanty 

1+ 

2+ 

3+ 

Zero AFB/1 length 

Zero AFB/1 length 

Zero AFB/1 length 

1–9 AFB/1 length or 100 HPF 

1–29 AFB/1 length 

1–19 AFB/1 length 

10–99 AFB/1 length or 100 
HPF 
1–10 AFB/1 HPF in at least 
50 fields 
>10 AFB/1 HPF in at least 20 
fields 

30–299 AFB/1 length 

20–199 AFB/1 length 

10–100 AFB/1 field on 
average 

5–50 AFB/1 field on average 

>100 AFB/1 field on average  >50 AFB/1 field on average 

43 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

4.8.1 ZN smear examination 

Examine one length of the smear (2 cm) or 100 fields with light microscope, using 1000x magnification. If less 
than 10 AFB are found in 100 fields, the number of AFB should be counted. For high positives, examination of only 
20 to 30 fields is sufficient. 

4.8.2 Auramine (fluorochrome) smear examination 

Examine one length of an auramine slide with a fluorescent microscope, using 200–250x magnification, to cover 30 
fields in one length, equivalent to 300 fields at 1000x magnification. Alternatively, 400x magnification can be used, 
covering 40 fields at this magnification. 

Negative report: Negative for acid-fast bacilli where no organisms observed in 100 fields. 

Positive report: Positive for acid-fast bacilli; provide AFB quantification. 

The results should be recorded in the TB laboratory register, and recorded on the sample examination request form as 
well as forwarded to the person requesting the sample examination [10]. 

Figures 4–5 give examples of smear microscopy using auramine and ZN staining. 

Figure 4. AFB smear microscopy of biological specimens 

A 

B 

Figure 5. AFB smear microscopy of M. tuberculosis cultures 

          D 

C 

E. 

A and E: Auramine stain 
B–D: Ziehl-Neelsen stain 

Images show cords. Pictures were kindly provided by Professor Zofia Zwolska, Head of the Microbiology Department, National 
Tuberculosis Reference Laboratory, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland. 

44 

 
 
 
 
 
 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

4.9 Quality control 

4.9.1 Quality control parameters 

Quality control in microscopy is a process for internally monitoring the performance of bench work in the 
laboratory. It consists of an effective and systematic process, ensuring that laboratory work is accurate, reliable 
and reproducible. This is done by assessing the quality of specimens; monitoring the performance of microscopy 
procedures, reagents and equipment; reviewing microscopy results and documenting the validity of microscopy 
methods. 

A positive and a negative control slide should be included in each run of stains, verifying the correct performance 
of the procedure as well as the staining intensity of the acid-fast organisms [14,15]. 

Table 10 shows the most common causes of error in smear microscopy. Control slides should be assessed prior to 
reading the patient smears to confirm the correctness of staining. If quality control slides are acceptable, patient 
smears can be read and reported. If the control slide(s) are unacceptable, the procedures and reagent 
preparations should be reviewed. After identifying and correcting the problem, all patient slides should be repeated 
with a new set of controls. The results of the quality control of reagents should be reported in the reagent 
preparation workbook. 

Table 10. Common causes of error in smear microscopy 

Errors 

Cause 
Smear too thick, detaching 
during staining 

False negative 

Smear too thin 

Poor staining 

Cross-contamination 

Action to be taken 
Improve homogenisation, reduce the material 
deposited. 
Increase the amount or make smear in 1x2 cm 
area only 
Check quality control of reagents, prepare new 
reagents, check dilution. 
Avoid contact between slides during staining 
procedure, do not use staining jars. 
Clean objective lens after reading each slide. 
Check water/solutions for environmental 
contamination. 

Red precipitates 

Prepare new solution. Filter before use. 

False positive 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

United States Department of Health and Human Services. Public health mycobacteriology: a guide for the 
level III laboratory. Atlanta, CDC; 1985. 

World Health Organization. Laboratory services in tuberculosis control. Part II: Microscopy. Geneva: WHO; 
1998. Available from: http://whqlibdoc.who.int/hq/1998/WHO_TB_98.258_(part2).pdf. 

World Health Organization. Maintenance and repair of laboratory, diagnostic imaging and hospital 
equipment. Geneva: WHO; 1994. Available from: http://whqlibdoc.who.int/publications/1994/ 
9241544635.pdf. 

World Health Organization. Maintenance manual for laboratory equipment. 2nd ed [Internet]. Geneva: 
WHO; 2008 [accessed 14 February 2011. Available from: http://www.who.int/entity/diagnostics_laboratory/ 
documents/guidance/guidance2. 

World Health Organization. Manual of basic techniques for a health laboratory, 2nd ed. Geneva: WHO; 
2003. 

Rieder HL, Van Deun A, Kam KM, Kim SJ, Chonde TM, Trébucq A, et al. Priorities for tuberculosis 
bacteriology services in low-income countries. 2nd ed. Paris: International Union against Tuberculosis and 
Lung Disease; 2007. 

Centers for Disease Control. Acid-fast direct smear microscopy training package [Internet]. Atlanta, CDC; 
2000 [accessed 14 February 2011]. Available from: http://stacks.cdc.gov/view/cdc/31282. 

Health Protection Agency, Standards Unit, Evaluations and Standards Laboratory. Investigation of 
specimens for Mycobacterium species. London: Health Protection Agency; 2006. Available from: 
http://www.hpa-standardmethods.org.uk/pdf_sops.asp. 

45 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

9. 

Collins C, Grange J, Yates M. Organization and practice in tuberculosis bacteriology. London: Butterworths; 
1985. 

10.  World Health Organization. Revised TB recording and reporting forms and registers – version 2006. Geneva: 

World Health Organization; 2006. Available from: http://www.who.int/tb/dots/r_and_r_forms. 

11.  World Health Organization: Fluorescent Light Emitting Diode (LED) microscopy for diagnosis of tuberculosis: 

WHO policy statement. Geneva: World Health Organization; 2010. Available from: 
http://www.stoptb.org/wg/gli/assets/documents/WHO%20Policy%20Statement%20on%20LED%20Microsc
opy%20FINAL%20March%202010.pdf. 

12.  World Health Organization. A roadmap for ensuring quality tuberculosis diagnostics services within national 
laboratory strategic plans. The Global Laboratory Initiative, Advancing TB Diagnosis. 2010. Available from: 
http://www.tbevidence.org/documents/rescentre/books/GLI_Roadmap_2010.pdf 

13. 

14. 

15. 

16. 

Stop TB Partnership and World Health Organization. New Laboratory Diagnostic Tools for TB Control. 
Geneva, World Health Organization, 2008. Available from: http://apps.who.int/tdr/publications/non-tdr-
publications/diagnostic-tool-tb/pdf/diagnostic-tool-tb.pdf 

Isenberg HD. Clinical microbiology procedures handbook. Washington: ASM Press; 1992. 

Cirillo D, Piana F, Vincent V, Angra P, Barrera L, Boulahbal F, et al. Training package on culture of acid-fast 
bacilli and drug-susceptibility testing of Mycobacterium tuberculosis. In: Tuberculosis Control Assistance 
Program. TB CAP Toolbox – TB CAP Laboratory Tools [CD ROM]. n.p.; 2009. Available from: 
http://www.tbcta.org//Uploaded_files/Zelf/NewLabTools1297631626.zip. 

Vincent V, van Deun A, Feldmann K, Barrera L, Paramasivan CN, Weyer K, et al. Guidance for countries on 
the preparation and implementation of TB laboratory standard operating procedures (WHO SOPs). In: 
Tuberculosis Control Assistance Program. TB CAP Toolbox – TB CAP Laboratory Tools 2009 [CD ROM]; 

17. 

Lumb R, Bastian I. Laboratory diagnosis of tuberculosis by sputum microscopy. Adelaide: Institute of 
Medical and Veterinary Science; 2005. p. 38. 

46 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

5. Culture tests for Mycobacterium 
tuberculosis complex 

Susana David, Vera Katalinić-Janković, Lanfranco Fattorini and Daniela Cirillo 

Revised by Emanuele Borroni, Enrico Tortoli and Vladyslav Nikolayevskyy (2015). 

5.1 Background and principles 

Bacteriological cultures can provide a definitive diagnosis of tuberculosis. The primary advantage of culture tests 
over sputum microscopy is their higher sensitivity, allowing for the detection of very low numbers of bacilli 
(approximately 10 bacilli/ml of sputum compared with at least 5000 bacilli/ml of sputum for microscopy). The use 
of cultures increases the potential of diagnosing TB at early stages of the disease. Culture tests are also used for 
the detection of treatment failures and for diagnosing extrapulmonary TB. The use of culture tests increases the 
number of TB cases found by 30–50%. Moreover, cultures are used for species identification and drug susceptibility 
testing (DST) [1,2]. 

As the EU has adopted the culture-based case definition, the main distinction in TB cases is between culture-
positive and -negative, and not sputum smear status. The first section of the European Standards for Tuberculosis 
Care (ESTC) 2012 [1] dedicated to the Standards for Diagnosis (ESTC 1 through ESTC 6) specifies the minimum 
requirements for obtaining a valid TB diagnosis in different settings or with various suspect types, both 
microbiological and clinical [1,2]. If this is not feasible, culture tests should at least be performed for: 

 

 
 
 
 

diagnosis of cases with clinical and radiological signs of pulmonary TB where smears are repeatedly 
negative 
diagnosis of extrapulmonary TB 
diagnosis of childhood TB 
diagnosis of TB among HIV-positive adults and children; and 
diagnosis and monitoring of MDR- and XDR-TB. 

Tuberculosis, although mainly a pulmonary disease, can affect any organ of the body. The isolation of the 
aetiological agent for effective microbiological diagnosis is dependent on: 

 
 
 

selection of the correct type of specimen 
the quality of the sample; and 
adequate use of storage and transportation procedures. 

Processing of inappropriate clinical specimens for mycobacterial cultures is a waste of both financial and human 
resources [6]. Clinical staff should be properly trained and accept only suitable specimens. 

Because mycobacteria are usually slow growing and require a long incubation time, a variety of other 
microorganisms can overgrow the cultures of specimens obtained from non-sterile sites. Appropriate pre-treatment 
and processing of samples, as well as the use of selective culture media is critical for eliminating contaminants 
while not seriously affecting the viability of mycobacteria [10]. 

5.2 Biohazards and biosafety in the TB laboratory 

Good microbiological techniques (GMT) – working methods designed to eliminate or minimise exposure to 
pathogens via, for example aerosols, splashes or accidental inoculation – are essential for minimising biohazards 
[13]. Nosocomial transmission of M. tuberculosis from specimens is a major concern for laboratory workers. All 
specimens suspected of containing M. tuberculosis should be handled with appropriate precaution at all times and 
opened only within an appropriate biosafety cabinet. Infectious aerosols are produced in the TB laboratory 
whenever a liquid suspension containing tubercle bacilli is handled. Biosafety measures in the laboratory are 
essential to protect workers against exposure to infectious aerosols. Please refer to Chapter 1 for more details on 
procedures and laboratory safety practices. 

Because of their viscosity, sputa are a minimal source of infectious aerosols. By contrast, aerosols produced during 
processing (especially during centrifugation) of homogenised sputa and during culture handling, must be minimised 
and therefore processed and contained in a biological safety cabinet. 

Classification of laboratory practices used for M. tuberculosis diagnosis should be based on a risk assessment 
(number and type of tests, prevalence of tuberculosis and of MDR-TB). Specimen processing for mycobacterial 
culture should be performed in a biological safety cabinet in at least a biosafety level 2 (BSL2) laboratory, whereas 
procedures involving manipulation of M. tuberculosis cultures (identification, sub-culturing and DST) must be 

47 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

performed in a biological safety cabinet in laboratories complying with BSL3 standards. All aerosol-generating 
procedures should be performed in a class I or II biological safety cabinet [9-11]. 

The health of laboratory workers should be regularly monitored by the employer. They should be educated about 
the symptoms of TB and, if symptoms arise, they should be provided with readily accessible free medical care in 
accordance to the national regulations. 

5.2.1 Minimum WHO recommendations for TB culture/drug 
susceptibility testing facilities 

WHO recommends that all specimen processing procedures are carried out in a laboratory built and equipped for 
BSL2. The minimum requirements for a BSL2 tuberculosis laboratory are: restricted access to the laboratory, the 
presence of a fully functional and maintained biological safety cabinet and an autoclave or other means of 
decontamination available in the same building. More information on biosafety is given in Chapter 1 [9-14]. 

Identification, subculturing, and drug susceptibility testing should be performed in a BSL3 containment room with 
an anteroom and directional airflow from functionally clean to dirty areas, with at least 6 to 12 air exchanges per 
hour. The containment room may be the blind end of a corridor, or formed by constructing a partition and door so 
that access to the laboratory is through an anteroom (e.g. double-door entry) or through the basic BSL2 laboratory. 
The autoclave should be in the vicinity of the laboratory so that the movement of contaminated materials is 
minimised. Biological safety cabinets have to be ducted to the outside or vented through a thimble. Recirculation of 
air from biological safety cabinets into the laboratory room and recirculation to other areas within the building are 
not permitted. Please refer to Chapter 1 for further detail on laboratory safety levels and conditions [14]. 

The decision to use additional PPE should be based on risk assessments. Risk assessments should be reviewed 
routinely and revised when necessary [7]. 

Masks and respirators 
One of the most common misconceptions is that a standard surgical mask can provide protection against M. 
tuberculosis infectious aerosols. Surgical masks made from poorly fitting porous material leave large gaps between 
the face and mask and therefore only help to prevent the spread of microorganisms from the wearer to others by 
capturing the large wet particles in the exhaled air. 

Although biological safety cabinets and airflow in the laboratory are the main means of protection against exposure 
to contaminated aerosols generated during culture and drug susceptibility testing activities, the need for additional 
personal protection must be considered in certain settings, such as when MDR-TB and/or HIV are prevalent. Staff 
may be HIV-infected and highly susceptible to contaminated aerosols [14]. 

Protection from inhalation of infectious aerosols can be provided by respirators, which are devices with the capacity 
to filter particles of 0.3–0.4 µm diameter and fit closely to the face to prevent leakage around the edges. The N95 
(FFP2) respirator is a lightweight, disposable nose and mouth respirator; it effectively filters out more than 95% of 
particles of diameter 0.3 µm and above. The FFP3 respirator removes more than 98% of such particles. Each user 
should be instructed in the proper use of the respirator and informed about its limitations. Respirators should be 
correctly fitted to the face to prevent leakage from around the face seal. This is done by placing the mask over the 
nose and mouth with the top elastic band over the crown of the head and the bottom elastic band over the back of 
the neck. The metal strip covering the nose should be firmly moulded over the bridge of the nose. Facial hair 
between the wearer's skin and the sealing surfaces of the respirator will prevent a good seal. Respirators should 
also be worn during emergency cleaning of spillages involving the release of viable organisms into the work area. 
Respirators should be stored in a convenient, clean and sanitary location and discarded after eight hours of 
(cumulative) use and not be kept for more than one week [7]. 

Gloves 
In accordance with international, universal procedures/guidelines, appropriate gloves should be worn for all 
procedures that involve the handling of body fluids. Gloves must be worn in case of hand injury/skin disease or 
when the risk of exposure to blood-borne pathogens is high; consequently, specimens resulting from invasive 
clinical investigation must be handled with gloves [12,14]. 

Gloves must be changed after every session that requires their use and after every interruption of the activity. 
Never wear gloves outside the laboratory. Every time hands are removed from the biological safety cabinet, gloves 
must be pulled off and discarded in a waste container in the safety cabinet [7,12,14]. 

Disposable latex, latex-free vinyl (clear) or nitrile gloves can be used and the correct size (small, medium or large) 
should be available for all individuals. Hypoallergenic gloves should be provided in case of allergy to latex proteins 
and/or to the corn-starch used for powder. Re-using single-use gloves is not advised. Used gloves should be 
discarded as contaminated material. Following the safe removal of gloves, wash hands immediately with water and 
liquid soap. Proper hand-washing with soap and adequate care in the handling of contaminated materials are 
critical elements of safe laboratory practice [14]. 

48 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Gowns 
Always wear a gown inside the laboratory (never outside) and change at least weekly. Long-sleeved back-opening 
gowns or overalls with narrow cuffs give better protection than laboratory coats and are preferred in microbiology 
laboratories. When worn, laboratory coats should be fully buttoned. An area of the laboratory must be designated 
for storage of used and new clothing. Laboratory gowns must be stored away from personnel clothing. Laundering 
services should be provided at/near the facility. Extra clothing should be available suitable for visitors, maintenance 
and emergency response personnel [7,12,14]. 

Always remove personal protective equipment in the following order: 

 
 
 

disposable gloves 
gown/coat/suit/overalls; and 
respirator/mask. 

5.3 Specimen collection, storage and transport 

5.3.1 Sample collection 

Proper specimen collection procedures and containers, adequate specimen volumes and appropriate transport 
conditions can all affect TB culture results. Correct labelling of specimens is critical. This includes patient and 
sample identification, sample type and date of collection. 

As a general rule, it is preferable that specimens are collected before starting specific treatments. Specimens 
should always be collected with care to avoid contamination by host or environmental microorganisms and 
submitted in sterile, leak-proof, disposable, appropriately labelled, laboratory-approved containers without any 
fixatives.  

If centrifugation is used for culture tests, the use of collection containers suitable for centrifugation should be 
considered. Decontamination and centrifugation in the collection container avoids having to transfer samples to 
another container [1-8]. 

Sputum samples 
Most specimens received by the laboratory are sputum samples. Patients should be clearly instructed on how to 
collect the sputum specimen; written instructions must be provided. 

A systematic review of 37 eligible studies [6] clearly showed that most TB cases (average 85.8%) were detected 
with the first sputum specimen. With the second sputum specimen, the average incremental yield was 11.9%; with 
the third specimen (when the first two were negative) the incremental yield was 3.1%. It is expected that 
laboratory analysis of two sputum smear samples will improve case-finding, reduce time to diagnosis, accelerate 
initiation of treatment and decrease the number of patients lost during the diagnostic process. Based on this 
evidence, WHO has recommended that two sputum samples in a single day be used to diagnose pulmonary TB in 
settings where a well-functioning EQA system is in place, the workload is high and human resources are limited. 

A good sputum specimen should be approximately 3–5 ml of recently-discharged material from the bronchial tree. 
It is usually thick and mucoid. It may be fluid and contain pieces of purulent material. The colour may vary from 
opaque white to green. Bloody specimens will appear reddish or brown. Clear saliva or nasal discharge is not 
suitable as a TB specimen, although saliva should not automatically be rejected: induced and follow-up sputa 
resemble saliva. To avoid contamination or dilution of a good sample, specimens should not be pooled. 

Other specimens 
Body fluids (spinal, pleural, pericardial, synovial, ascitic, blood, pus and bone marrow) should be aseptically 
collected in sterile containers using aspiration techniques or surgical procedures. Pleural effusion is a suboptimal 
specimen: tubercle bacilli are mainly in the pleural wall and not in the fluid. The minimum volume for pleural 
effusion is 20–50 ml. A pleural biopsy specimen is ideal. 

For fluids that may clot, sterile potassium oxalate (0.01–0.02 ml of 10% neutral oxalate per ml fluid), heparin (0.2 
mg/ml), or sodium citrate (two drops of 20% sodium citrate for every 10 ml of fluid) should be added as an 
anticoagulant to the culture. 

Aseptically collected tissues should be placed in sterile containers without fixatives or preservatives and transported 
quickly to the laboratory. For prolonged transportation, dehydration should be prevented by adding sterile saline 
and maintaining a temperature of 4–15°C. 

Urine is expected to be contaminated. To minimise excessive contamination of urine specimens, external genitalia 
should be washed before specimen collection. Once received in the laboratory, a urine sample must either be 
processed immediately or centrifuged and the pellet refrigerated. As excretion of tubercle bacilli is intermittent, 
three consecutive early-morning midstream specimens must be collected. 

49 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Other respiratory specimens that can be submitted to the laboratory for mycobacterial culture are bronchial 
secretion (minimum volume 2–5 ml) and bronchial alveolar lavage samples (minimum volume 20–50 ml). 
Transbronchial and other biopsies taken under sterile conditions should be kept wet during transportation by 
adding 0.5–1 ml sterile 0.9% saline. 

In children who produce little, if any sputum, aspiration of the early-morning gastric juice can be used for TB 
diagnosis. The gastric aspirate should be transported immediately to the laboratory and neutralised by adding 
100 mg of sodium bicarbonate. 

5.3.2 Storage of specimens  

Specimens should be correctly collected and delivered as quickly as possible to the laboratory. Every effort must be 
made to organise and expedite specimen transportation and processing. Although TB bacilli can survive in sputum 
for one week in the absence of preservatives, the probability of successfully culturing the bacilli decreases with 
time and this is especially critical for paucibacillary specimens. If specimens cannot be transported to the 
laboratory within one hour, it is recommended to store them at 4°C. This does not apply to whole blood specimens, 
which are not to be refrigerated. On arrival at the laboratory, specimens should again be refrigerated until they can 
be processed. The delay between collection and inoculation should not exceed seven days. 

5.3.3 Transportation of specimens  

Packaging of infected specimens that are to be sent by surface or air mail must be carried out according to national 
biosafety and biosecurity guidelines or international rules. For international transfer of infectious substances, the 
International Air Transport Association (IATA) should be contacted [7]. 

Specimens and cultures should be packaged in a three-component packaging consisting of: 

 
 
 

a leak-proof primary receptacle(s) 
a leak-proof secondary packaging; and 
an outer packaging of adequate strength for its capacity, mass and intended use. 

For the purposes of transport, infectious substances are defined as substances which are known or reasonably 
expected to contain pathogens [7,8]. Category A (UN2814) corresponds to an infectious substance which is 
transported in a form that, when exposure to it occurs, is capable of causing permanent disability, and/or life-
threatening or fatal disease in otherwise healthy humans or animals. All other infectious substances as well as 
human biological specimens belong to Category B (UN3373). 

Cultures of M. tuberculosis belong to Category A. However, for surface transport, when M. tuberculosis cultures are 
intended for diagnostic or clinical purposes, they may be classified as category B. For surface transport there is no 
maximum quantity per package. 

For air transport: 

 
 

no primary receptacle should exceed 1 l (for liquids) or the outer packaging mass limit (for solids); and 
the volume shipped per package should not exceed 4 l or 4 kg. 

These quantities exclude ice, dry ice or liquid nitrogen when used to keep specimens cold. 

5.4 Homogenisation and decontamination of specimens 

Most (but not all) specimens are considered contaminated. Pulmonary specimens including sputum, bronchial 
secretions, bronchoalveolar lavage, bronchial aspirates and brushings are usually contaminated by normal host 
microbiota. Extrapulmonary specimens may be divided into two main groups according to the extent of 
contamination: 

 
 

Aseptically collected specimens, usually free from other microorganisms (sterile). 
Specimens contaminated by normal flora or specimens not collected aseptically (not sterile). 

Normally, contaminated extrapulmonary specimens are gastric lavage, laryngeal aspirates, urine, skin, autopsy 
materials, and uterine mucosa. Sterile specimens include pus from cold abscess, CSF, synovial or other cavity body 
fluids, as well as surgical biopsies. 

Contaminated specimens must be subjected to rigorous decontamination procedures that liquefy the organic debris 
and eliminate the unwanted normal flora. Normal flora would rapidly overgrow the entire surface of the medium 
and consume it before the TB bacilli started to grow. Specimens must be homogenised to free the bacilli from the 
mucus, cells or tissue in which they may be embedded. 

Digesting/decontaminating agents are to some extent toxic to tubercle bacilli and therefore to minimise the 
number of dead mycobacteria, the digestion/decontamination procedure must be followed precisely. A proportion 
of cultures will be contaminated by other organisms: a contamination rate of 3–5% is acceptable on solid media. 
Cultures in liquid media may show higher contamination rates (5–10%). Furthermore, if specimens (especially 
50 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

sputum) take several days to reach the laboratory, the contamination rate may be higher. At present, new 
commercial kits are available, containing transportation media supplemented with decontamination solutions for 
longer shipments between countries or cities. These may help to reduce the proportion of contaminated cultures 
due to long shipments and increase the proportion of positive cultures among those samples which are not 
inoculated at the point of collection. A contamination rate that approaches 0 indicates that the decontamination 
procedure was too harsh. 

5.4.1 Digestion and decontamination of sputum samples  

Digestion and decontamination using the sodium hydroxide (modified Petroff) 
method 
Sodium hydroxide is toxic, both for contaminants and for tubercle bacilli; strict adherence to the indicated timings 
is therefore essential. This decontamination procedure can only be used for samples which will then be inoculated 
on solid media. 

Reagents: 

 
 

Sodium hydroxide (NaOH) solution, 4% 
Phosphate buffer 0.067 mol/l, pH 6.8 

Sodium hydroxide (NaOH) solution, 4%: 

 
 

Sodium hydroxide pellets (analytical grade): 4 g 
Distilled water: 100 ml 

Dissolve NaOH in the distilled water. Aliquot in 2 ml quantities. Sterilise by autoclaving at 121ºC for 20 minutes. 

Phosphate buffer, 0.067 mol/l, pH 6.8: 

 

Stock solution A: disodium phosphate, 0.067 mol/l 

Dissolve 9.47 g of anhydrous Na2HPO4 in 1 l of distilled water. 

 

Stock solution B: monopotassium phosphate, 0.067 mol/l 

Dissolve 9.07 g of KH2PO4 in 1 l of distilled water. 

Mix 50 ml of solution A and 50 ml of solution B. Use a pH meter to confirm that the correct pH for the buffer is 
reached. Adjust as necessary, using 10% phosphoric acid or 10% sodium hydroxide. 

Aliquot in the volumes required for adding to a single centrifugation tube (e.g. 50 ml amounts if 50 ml centrifuge 
tubes are used), discarding the extra volume. Sterilise by autoclaving at 121ºC for 20 minutes. Leftover volumes of 
buffer can then be pooled and sterilised again for further use. 

Procedure: 

 

 
 
 

 
 
 
 
 

 
 

 

If sputum has not already been collected in centrifuge tubes, select sterile plastic screw-top centrifuge 
tubes (one for each specimen). 
With a permanent marker, write the number of the specimen on the wall of the tube (not on the cap). 
Write the number of each specimen and the inoculation date on two tubes of media. 
Mark the volume of sputum on the centrifuge tube (at least 2 ml, not more than 5 ml). Add an equal 
volume of 4% NaOH and tighten the screw-cap. 
Vortex to digest. 
Allow to stand for 15 minutes at room temperature. 
Fill the tube to within 2 cm of the top (e.g. to the 50 ml mark on the tube) with phosphate buffer. 
Centrifuge at 3000 g for 15 minutes. 
Carefully pour off the supernatant through a funnel into a discard can containing 5% phenol or another 
mycobacterial disinfectant. 
Re-suspend the deposit in approximately 0.3 ml phosphate buffer. 
Inoculate the deposit on two slopes of egg-based medium labelled with the ID number. Use a pipette to 
inoculate each slope with 3–4 drops (approximately 0.1–0.15 ml). 
Smear one drop on a slide, marked with the ID number, for microscopic examination. 

Digestion and decontamination using the N-acetyl-L-cysteine-sodium hydroxide 
(NALC-NaOH) method 
The most widely used method for the digestion and decontamination of contaminated specimens is the N-acetyl-L-
cysteine-sodium hydroxide (NALC-NaOH) method. 

Decontamination using NALC-NaOH is based on the mucolytic properties of N-acetyl-L-cysteine (NALC) which 
enable the decontaminating agent, sodium hydroxide, to be used effectively at a low, final concentration. 
Consequently, the NALC method results in more positive cultures than other methods, as it only kills about 30% of 

51 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

the tubercle bacilli in clinical specimens; a lower NaOH concentration means that contamination rates may be 
higher than for other decontamination methods. The time needed to process a single specimen is approximately 40 
minutes, while 20 specimens would take approximately 60 minutes. 

This method is suitable for cultures on both solid and liquid media. However, the disadvantages of the method are 
that NALC loses activity and must therefore be made fresh every day. Commercially prepared solutions are 
available, but expensive. 

After exposure to the decontaminant and subsequent centrifugation, it is essential that the sediment is re-
suspended in a 1:10 dilution of buffer (or water) to reduce the concentration of any toxic components that may 
inhibit the growth of TB bacilli. 

As a measure of precaution, an aliquot of the sediments should be kept for one week in the refrigerator and re-
decontaminated if the inoculated cultures show signs of contamination. Optionally the sediment can be frozen 
(- 20°C) in a screw-cap sterile 1.5-2 ml vial that is properly labelled.  

Reagents N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) method: 

Sodium hydroxide-citrate solution 

Solution A: Sodium hydroxide 4% 

Sodium hydroxide pellets (analytical grade) 
Distilled water 

Dissolve NaOH in the distilled water 

Solution B: Trisodium citrate 3H2O 2.94% 

Trisodium citrate 3H2O 
Distilled water 

Dissolve trisodium citrate 3H2O in the distilled water. 

40 g 
1000 ml 

29.4 g 
1000 ml 

Mix solutions A and B, aliquot in 100 ml quantities, and sterilise by autoclaving at 121°C for 15 minutes. Store at 
4°C in refrigerator.  

N-acetyl-L-cysteine (NALC) 

NALC-NaOH solution should be freshly prepared for daily use only.  

Prepare by adding 0.5g NALC to 100 ml of the sodium hydroxide-citrate solution just before use: aliquot in 4 ml 
amounts. 

Phosphate buffer, 0.067 mol/l, pH 6.8 

See above for preparation. 

Sputum processing 
Sputum specimens are not to be pooled because of the risk of cross-contamination. Always digest/decontaminate 
the whole specimen – do not attempt to select portions of the specimen as is done for direct microscopy. Gently 
decant from the specimen container into the centrifuge tube. If the specimen is too viscous to pour, an equal 
volume of digestant/decontaminant can be added to the sputum in the specimen container before the mixture is 
poured carefully into an appropriate screw-top centrifuge tube. 

Sputa are not to be processed in batches of more than 6–8 as the method is strictly time-dependent. 

Procedure: 

If sputum has not already been collected in centrifuge tubes, select sterile plastic screw-top centrifuge 
tubes (one for each specimen). 
With a permanent marker, write the number of the specimen on the wall of the tube (not the cap). 
Write the number of each specimen and the inoculation date on two tubes of media. 
Transfer the sputum (at least 2 ml, but no more than 5 ml) into a centrifuge tube. Add an equal volume of 
NALC-NaOH solution. 
Tighten the cap of the tube and shake or vortex. Mix for no more than 20 seconds. 
Keep at 20–25°C for 15 minutes to decontaminate. 
Fill the tube to within 2 cm of the top (e.g. the 50 ml mark on the tube) with 0.067 mol/l phosphate buffer 
(pH 6.8) or distilled water. Vortex mix. 
Centrifuge at 3000g for 15 minutes. 
Carefully pour off the supernatant into a discard bottle containing the appropriate disinfectant. 

 

 
 
 

 
 
 

 
 

52 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

 

Re-suspend the deposit and inoculate onto two slopes of LJ medium (and one slope of LJ with pyruvate if 
needed) or into liquid medium. Using a pipette (not a loop), inoculate each slope with 3–4 drops (0.2–0.4 
ml). Smear one drop on a slide (marked with the ID number) for microscopic examination. 

5.4.2 Digestion and decontamination of specimens other than sputum 

Laryngeal swabs 
Smear examination is not done for laryngeal swabs. Swabs yield little material: as much of the material as possible 
must be collected and not wasted.  

 
 
 
 
 
 

 
 
 

Swabs must be cultured on the day they are received using sterile precautions. 
Use sterile forceps to transfer the swab to a sterile centrifuge tube. 
Add 2 ml of sterile distilled water. 
Decontaminate according to NaOH-NALC method (see above, Section 5.4.1). 
Before adding the phosphate buffer solution, remove the swab from the tube using sterile forceps. 
Fill the tube to within 2 cm of the top (e.g. the 50 ml mark on the tube) with phosphate buffer, 0.067 mol/l, 
pH 6.8 and mix the contents by inversion. 
Centrifuge at 3000g for 15 minutes. 
Carefully pour off the supernatant into a discard bottle containing an appropriate disinfectant. 
Inoculate the deposit on two slopes of LJ medium (and one slope of LJ with pyruvate, if needed) or in liquid 
medium. Using a pipette (not a loop), inoculate each slope with 3–4 drops. 

Gastric lavages 
Gastric lavage specimens should be processed as soon as possible after collection; acidity can kill mycobacteria in 
the specimen so gastric lavage specimens must be processed within four hours. The gastric aspirate should be 
collected in a tube containing 100 mg of sodium bicarbonate for neutralisation and should be transported 
immediately to the laboratory. Proceed as for sputum. 

If the specimen is watery, centrifuge at 3000g for 15 minutes, pour off the supernatant, re-suspend the sediment 
in 5 ml of sterile distilled water and proceed as for sputum. 

Mucopurulent materials 
Handle as for sputum when the volume is 10 ml or less. 

Handle as for mucoid gastric lavage when the volume is more than 10 ml. 

Fluid materials 
If the specimen has been collected aseptically, centrifuge and inoculate the sediment directly onto culture media, 
preferably liquid medium. 

Materials that should not be decontaminated are: 

 
 
 
 
 

spinal, synovial or other cavitary body fluids 
bone marrow 
pus from cold abscesses 
surgically resected specimens (excluding autopsy material); and 
material obtained from pleural, liver and lymph nodes as well as biopsies (if not fistulised). 

To maximise the recovery rate, the entire CSF volume (or other small volume of aseptically collected fluid) should 
be cultured, preferably in liquid medium. 

If the specimen was not aseptically collected: 

 
 

Handle as for sputum when the volume is 10 ml or less. 
Handle as for fluid gastric lavage when the volume exceeds 10 ml. 

Tissue 
If a biopsy needs to be processed for smear and culture, it is necessary to homogenise the biopsy in a sterile 
porcelain mortar or preferably in a small, non-reusable tissue grinder with 2–5 ml of sterile saline. 

Mortars, pestles and tissue grinders must be cleaned and sterilised thoroughly to prevent false-positive results or 
contamination due to organisms left over from previous specimens. Lymph nodes, biopsies and other surgically 
resected tissue should be cut into small pieces with a sterile scalpel or scissors. Homogenise the specimen in a 
sterile porcelain mortar or tissue grinder using 5 ml sterile saline and a small quantity of sterilised sand. Inoculate 
the suspension onto culture media. 

53 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

5.5 Culture media: principles 

As M. tuberculosis grows slowly, with a generation time of 18–24 hours (other bacteria reproduce within minutes), 
usual bacteriology techniques are not applicable to mycobacterial cultures. Moreover, growth requirements are such 
that M. tuberculosis will not grow in primary isolation on simple, chemically-defined media. The only media that 
allows for abundant growth are egg-enriched media containing glycerol and asparagine, and agar or liquid media 
supplemented with serum or bovine albumin. Many different media have been developed for M. tuberculosis 
growth and are generally classified into two main groups: solid media (egg- and agar-based) and liquid media. 
Antibiotics can be added to culture media in order to prevent the growth of non-specific flora. 

Both solid and liquid media are recommended for M. tuberculosis isolation from biological samples. An advantage 
of solid over liquid media is that colonies of mixed cultures and contaminants can be observed while liquid media 
promotes a faster growth of mycobacteria. 

The choice of media depends primarily on the type of specimen. Non-selective media are recommended for use 
with samples from normally sterile sites (bone marrow, tissue biopsy samples, cerebrospinal fluid and other body 
fluids etc.), while selective media, that contain antimicrobial agents to prevent growth by contaminating bacteria 
and fungi, are recommended for use with contaminated (or potentially cotaminated) specimens (sputum, abscess 
contents, bronchial washings, gastric lavage fluid, urine, etc.) [1,2].  

The most commonly used non-selective media are: 

 
 
 

egg-based media: Löwenstein-Jensen (LJ) medium and Ogawa medium 
agar-based media: Middlebrook 7H10 and Middlebrook 7H11; and 
liquid media: Middlebrook 7H9 broth. 

Other commonly used selective media available in some countries are: 

 

 

 

egg-based media: Gruft modification of LJ (containing malachite green, penicillin and nalidixic acid as 
selective agents, and Mycobactosel LJ (containing malachite green, cycloheximide, lincomycin and nalidixic 
acid as selective agents) 
agar-based media: selective 7H11 (Mitchison’s medium), containing carbenicillin, amphotericin B, polimixin 
B and trimethoprim as selective agents; and 
liquid media: in general they contain a modified Middlebrook 7H9 broth plus a mixture of antimicrobial 
agents. Several automated systems have been commercially developed for rapid detection of mycobacteria 
in liquid medium: 
 
 
 

BACTEC µGIT 960 system (BD [Becton, Dickinson and Company] Diagnostic Systems) 
ESP Culture System II (Trek Diagnostic Systems 
MB/BacT (bioMérieux). 

5.6 Solid media 

5.6.1 Egg-based media 

LJ medium, which contains malachite green as an inhibitor of non-mycobacterial organism, is the most commonly 
used egg-based medium, especially for sputum culture. LJ is user-prepared or commercially prepared in slant 
tubes. LJ containing glycerol favours M. tuberculosis growth, while LJ without glycerol but containing sodium 
pyruvate enhances M. bovis growth. Both media should be used in geographical regions where patients may be 
infected with either organisms [3]. Ogawa medium is LJ without asparagine. Non-selective egg-based media can 
be stored in the refrigerator for several months provided that the tube caps are tightly closed to minimise 
evaporation.  

A disadvantage of egg-based media it that when contamination does occur it may involve the entire slant surface, 
so the culture is generally lost. If specimens contain few bacilli it may take three to eight weeks before cultures 
become positive.  

5.6.2 Agar-based media 

These media are prepared in slant tubes or plates and are less likely than egg-based media to become 
contaminated. Middlebrook 7H10 and 7H11 media are usually prepared in the laboratory from commercially 
available agar-powdered bases, with the addition of Middlebrook oleic acid-albumin-dextrose-catalase (OADC) 
enrichment. Because of the transparency of 7H10 and 7H11 plates, M. tuberculosis micro colonies with typical cord 
formation can be detected and counted using a microscope as early as one week after incubation. Moreover, 
visibility of colonial morphology on agar plates is better than on egg-containing slants, aiding the identification of 
mycobacteria. Middlebrook 7H11 is preferable to 7H10 because it contains 0.1% casein hydrolysate, a substance 
favouring the recovery of isoniazid-resistant mycobacteria. Furthermore, 7H11 is also better for growing multi-drug 
resistant (MDR) strains as these may not grow at all on 7H10 agar plates. 

54 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

A disadvantage of Middlebrook media is that the surface dries more rapidly than egg-based media. It is important 
to know that daylight, heating and storage at 4°C for more than four weeks may cause the release of 
formaldehyde in a sufficient concentration to inhibit the growth of mycobacteria. 

5.6.3 Liquid media 

Liquid media offer a considerable time advantage over solid media: 7–14 days in Middlebrook 7H9 liquid medium, 
compared with 18–28 days in Middlebrook 7H11 agar, or 21–42 days in LJ medium [5].  

One of the most widely used automated systems for rapid detection of mycobacteria in liquid medium is the BACTEC 
µGIT 960 system [2]. The system’s culture tubes consist of modified Middlebrook 7H9 broth, a growth supplement, 
and an antimicrobial agent mixture. A similar principle is used in the ESP Culture System II and the MB/BacT system. 
In the BACTEC 960 system and ESP Culture System II, M. tuberculosis growth is detected by the rate of oxygen 
consumption within the headspace of the cultures; in the MB/BacT system, a colorimetric sensor detects the 
production of CO2 dissolved in the culture medium. 

5.6.4 Quality control of media 

Quality control of the media is needed to ensure that the strain isolated from a specimen is from the patient and 
not a contaminant present in the ingredients of the medium. The description below mainly applies to quality control of 
solid media, as it is on such media that colonies are visible to the eye and species identification is therefore possible. 

Commercially prepared media do not need to be quality controlled for sterility, growth and selectivity, provided that 
documentation of the manufacturer’s quality control procedures is obtained [12]. The information should include the 
preparation date, the lot number, the expiration date, the test organisms used, the date of testing and the result. In 
all other cases (user-prepared media and when documentation of sterility, growth and selectivity is not provided), the 
media must be checked for: 

 
 
 

medium conditions: colour, dehydration, contamination, bubbles 
sterility: incubating from 1–3% of each batch at 35–37°C in 5 to 10% CO2 for up to 21 days 
performance: by testing growth of positive and negative control strains. 

The organisms used as positive controls are M. tuberculosis H37Ra (ATCC 25177), M. kansasii ATCC 12478, M. 
scrofulaceum ATCC 19981, M. intracellulare ATCC 13950 and M. fortuitum ATCC 2841. Escherichia coli ATCC 25922 
is used to demonstrate partial inhibition by non-selective media and complete inhibition by selective media. 

Procedure [1,2]: 

 
 

 

Prepare a 0.5 McFarland suspension of the organisms in 7H9 broth. 
Inoculate media with 10µl of the control suspension using a pipette or a calibrated loop. To test selective 
properties of the media, inoculate them with 10µl of 1:10 suspension in sterile 0.85% NaCl. Incubate all 
media at 35–37°C in 5–10% CO2 for up to 21 days. 
Expected results are as follows: 

Positive controls 

M. tuberculosis ATCC 25177 

M. kansasii ATCC 12478 

M. scrofulaceum ATCC 19981 

M. fortuitum ATCC 2841 

M. intracellulare ATCC 13950 

Result 

Growth on all media 

Growth on all media 

Growth on all media 

Growth on all media 

Growth on all media (not included when testing selective 
media containing penicillin or carbenicillin) 

Negative control 

Result 

Escherichia coli ATCC 25922 

Partial inhibition in non-selective media, 
total inhibition in selective media 

5.7 Culture tube inoculation 

5.7.1 Solid media 

In media that is purchased ready-to-use, condensed moisture is frequently observed on the culture slants and it is 
advisable to remove it before use. Each slant should be inoculated with 0.2–0.4 ml (2–4 drops or four loopfuls) of 

55 

 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

the centrifuged sediment. The use of sterile disposable Pasteur pipettes is highly recommended. The inoculum 
should be distributed over the entire surface of the slant. 

At least two slopes of LJ medium per specimen should be inoculated with 0.2 ml of each sediment. In areas where 
M. bovis is isolated, an additional slope containing pyruvate is recommended. Using a ready-made commercially 
available egg-based media supplemented with antibiotic mixture may help to reduce contamination rates. Too little 
inoculum is a common cause of false-negative results. In the upper part of the slant the medium is thin and 
dehydrates readily; if mycobacteria are seeded only on this upper section, they might not grow, again leading to 
false-negative results. 

5.7.2 Liquid media 

Inoculation on liquid media should be performed under rigorous sterile conditions to avoid the risk of 
contamination. Liquid media is more susceptible to contamination than solid media and therefore needs to be 
supplemented with a mixture of specific antibiotics to kill the contaminants. These antibiotic mixtures are available 
from commercial companies selling culture media for automated culture systems. 

Each properly labelled liquid culture tube should be inoculated with 0.5 ml of sediment and the sediment must be 
deposited under the surface of the medium, keeping the tube tilted at an angle of 45°. The tube is then returned 
to a vertical position, leaving the inoculum below the surface of the liquid. 

5.8 Culture incubation 

All cultures should be incubated at 35–37°C. Always check the temperature indicator before incubating the 
cultures. The cultures should be incubated until growth is observed, or discarded as negative after 8 to 12 weeks 
(6 weeks if liquid media is used). 

Inoculated solid cultures should be incubated with caps loosened in a slanted position for at least one week to 
ensure an even distribution of the inoculum. Caps should then be tightened to prevent desiccation of the media 
and, if space is needed in the incubator, the tubes can be placed upright. Tops should be tightened to minimise 
evaporation which can result in the media drying out. 

5.9 Culture examination 

All cultures should be examined 48 hours after inoculation in order to: 

 
 
 

check absorption of inoculated liquid 
tighten caps to prevent drying out of media; and 
detect early contaminants. 

Cultures should then be examined on a weekly basis or, if this is not feasible, at least three times during the eight-
week incubation period (Figure 6). 

 
 

 

Seven-day check: To detect rapidly growing mycobacteria. 
Three-to-four-week check to detect positive cultures of M. tuberculosis as well as other slow-growing 
mycobacteria. 
End of culture check (after eight weeks) to detect very slow-growing mycobacteria, including M. 
tuberculosis, before discarding and reporting the culture as negative. 

56 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Figure 6. Minimal examination schedule for solid cultures 

Source: Culture, DST and quality assurance package, WHO [14] 

The different kinds of contaminants that should be considered are non-tuberculous mycobacteria, fungi, bacteria 
and yeasts. 

After ZN staining, the culture should be handled according to the results: 

 

 

 
 

Presence of AFBs only in the deposit with no non-AFBs indicates pure growth of mycobacteria – the deposit 
should be processed for identification and drug susceptibility testing (inoculation of a non-selective agar 
plate, such as blood agar, can be used to check for purity). 
Presence of AFBs with non-AFBs in the deposit indicates contamination of the possible growth of 
mycobacteria – the deposit should be processed for decontamination and culture on solid media. 
No AFBs and only non-AFBs in the deposit indicate growth of contaminants – the deposit should be discarded. 
Any presence of contaminants should be recorded in the laboratory register and if the culture is discarded, 
it should be reported as a ‘contaminated culture’.  

Evaluation of the contamination rate should be performed every three to six months for quality assurance 
purposes. A contamination rate of 3–5% is considered a good balance between the need to kill contaminating 
bacteria and the need to keep the majority of tubercular mycobacteria present in the sample. A contamination rate 
of 0–1% may indicate too strong a decontamination process. The contamination rate should refer to the number of 
contaminated tubes, not to the number of registered specimens. 

Common contaminants are detailed below [4]: 

Non-tuberculous mycobacteria: 

 
 
 

Fast- or slow-growers 
Acid-fast bacilli 
Not usually arranged in cords. 

Fungi: 

 
 
 

Usually slow-growers 
Non-acid-fast 
Hyphae are thicker than mycobacteria. 

Bacteria: 

 

Usually non-acid-fast except for some closely related genera (Gordonia, Tsukamurella, Nocardia, 
Rhodococcus, Dietzia) and Legionella micdadei. 

Yeast: 

 

Usually non-acid-fast. 

Oocystis: 

 

Usually non-acid-fast except for Cryptosporidium, Isospora, Cyclospora. 

57 

Inoculation02 days•Make sure that liquid has completely evaporated, tighten caps in order to prevent drying out of media (solid)•Detect contaminants (solid and liquid)•On solid detectrapidly growing mycobacteria•On liquid possible MTB or NTM1 weekDetect positive cultures of M. tuberculosisas well as other slow-growing mycobacteria2 to 4 weeks•Detect very slow-growing mycobacteria, including M. tuberculosis•End of culture examination for negative report8 weeks•Liquid culture: detect slow growing mycobacteria•Liquid culture: end of culture examination for negative report6 weeks(solid: weekly preferable)Liquid: daily preferable 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

10. 

11. 

Migliori GB, Zellweger JP, Abubakar I, Ibraim E, Caminero JA, De Vries G, et al. European Union standards for 
tuberculosis care. Eur Respir J. 2012 Apr;39(4):807-19 

De Kantor IN, Kim SJ, Frieden T, Laszlo A, Luelmo F, Norval PY, et al. Laboratory services in tuberculosis 
control. WHO Global Tuberculosis Programme. WHO/TB/98.258. Geneva: WHO; 1998 

Leão SC, Martin A, Mejia GI, Palomino JC, Robledo J, Telles MAS, et al. Practical handbook for the 
phenotypic and genotypic identification of mycobacteria. Antwerp: TropMed Central Antwerp; 2004. 
Available from: http://www.esmycobacteriology.eu/PDF%20files/foreword.pdf. 

Iseman MD. A clinical guide to tuberculosis. Philadelphia: Lippincott Williams & Wilkins, 2000. 

Mase SR, Ramsay A, Ng V, Henry M, Hopewell PC, Cunningham J, et al. Yield of serial sputum specimen 
examinations in the diagnosis of pulmonary tuberculosis: a systematic review. Int J Tuberc Lung Dis. 2007 
May;11(5):485-95. 

Cirillo D, Piana F, Vincent V, Angra P, Barrera L, Boulahbal F, et al. Training package on culture of acid-fast 
bacilli and drug-susceptibility testing of Mycobacterium tuberculosis. In: Tuberculosis Control Assistance 
Program. TB CAP Toolbox – TB CAP Laboratory Tools [CD ROM]. n.p.; 2009. Available from: 
http://www.tbcta.org//Uploaded_files/Zelf/NewLabTools1297631626.zip. 

World Health Organization. Guidance on regulations for the Transport of Infectious Substances 2013–2014. 
Geneva: WHO; 2012 Available from: http://apps.who.int/iris/bitstream/10665/78075/1/WHO_HSE_GCR_ 
2012.12_eng.pdf. 

Vincent V, van Deun A, Feldmann K, Barrera L, Paramasivan CN, Weyer K, et al. Guidance for countries on 
the preparation and implementation of TB laboratory standard operating procedures (WHO SOPs). In: 
Tuberculosis Control Assistance Program. TB CAP Toolbox – TB CAP Laboratory Tools 2009 [CD ROM].  

Health Protection Agency, Standards Unit, Evaluations and Standards Laboratory. Investigation of 
specimens for Mycobacterium species. London: Health Protection Agency; 2006. Available from: 
https://www.gov.uk/government/publications/smi-b-40-investigation-of-specimens-for-mycobacterium-
species. 

Richmond JY, McKinney RW, editors. Primary containment for biohazards: selection, installation and use of 
biological safety cabinets. 2nd ed. Washington, D.C.: US Department of Health and Human Services; 2000. 

Drobniewski FA, Hoffner S, Rusch-Gerdes S, Skenders G, Thomsen V; WHO European Laboratory 
Strengthening Task Force. Recommended standards for modern tuberculosis laboratory services in Europe. 
Eur Respir J. 2006 Nov;28(5):903-9. 

12.  World Health Organization. Laboratory biosafety manual. Third Edition. Geneva: WHO; 2004. 

13. 

Tuberculosis Control Assistance Program. TB CAP Toolbox – TB CAP Laboratory Tools 2009 [CD ROM]. 
Available from: http://www.tbcta.org//Uploaded_files/Zelf/NewLabTools1297631626.zip. 

14.  World Health Organization. Tuberculosis laboratory biosafety manual. Geneva: WHO; 2012. Available from: 

http://apps.who.int/iris/bitstream/10665/77949/1/9789241504638_eng.pdf. 

58 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

6. Identification of Mycobacterium 
tuberculosis and drug resistance in cultures 
and sputum using molecular assays and 
immunoassays 

Doris Hillemann, Sarah Mitchell, Francis Drobniewski 

Revised by Doris Hillemann (2014) 

6.1 Background and principles 

Historically, mycobacteria have been directly detected in patient specimens by staining and subsequent microscopy. 
This is a rapid and cheap method; however, it requires a high bacterial count in the specimen for a reliable result. 
In addition to the low sensitivity, differentiation of the microorganisms is rarely possible using microscopy. Hence, 
the need to culture mycobacteria in special liquid and solid media, a method which is still the gold standard for 
detecting mycobacteria in different specimens (Chapter 5). However, the culture of mycobacteria can take between 
six and eight weeks as TB bacilli and many other mycobacteria grow very slowly. Therefore, early and specific 
treatment of the patient is delayed with standard biochemical and growth-based differentiation tests.  

Molecular biology is now becoming more important in the diagnosis of mycobacteria. It supports culture either by 
serving as a rapid direct test on specimens or by enabling a rapid and unequivocal species differentiation from 
culture material. Nucleic-acid-based methods have largely displaced the classical methods. 

Molecular genetic tests offer considerable time advantages in the identification of mycobacteria, enabling a more 
rapid initiation of resistance tests and specific treatment. They are useful tools for the detection and differentiation 
of mycobacteria from cultures and can have a high specificity and sensitivity. It should be noted however, that they 
cannot/should not replace the currently endorsed standard methods of detecting mycobacteria and determining 
drug-susceptibility patterns. Instead they should be used to support the diagnostic work-up. Test results should 
always be confirmed using the standard methods.  

This chapter includes methods for the identification of mycobacteria as well as drug susceptibility testing from 
culture and specimens.  

6.2 Procedure 1: Chromatographic immunoassay for the 
qualitative detection of Mycobacterium tuberculosis 
complex from cultures  

Assays used: Capilia TB-neo, TAUNS Laboratories Co, Numazu, Japan, and BD µGIT TBc Identification Test, BD 
(Becton, Dickinson and Company) Diagnostic Systems, Sparks, MD, USA. 

6.2.1 Introduction 

Definite diagnosis of TB can be made by identifying M. tuberculosis complex organisms from a clinical sample after 
growth in solid or liquid media. Since M. tuberculosis complex strains (with the exception of some sub-strains of M. 
bovis BCG) but not non-tuberculous mycobacteria specifically and predominantly secrete the MPB64 protein 
(mycobacterial protein fraction from BCG of Rm 0.64), this can be used to discriminate between M. tuberculosis 
complex and non-tuberculous mycobacteria. Immunochromatographic assays based on the reaction of monoclonal 
antibodies against MPB64 have been developed and evaluated [1-3]. 

6.2.2 Materials 

No special equipment is required for the test; it is sufficient to use the test plates provided by the manufacturer, a 
100 µl pipette, and a timer. The test plates consist of a placing area, a test area containing the anti-MPB64 
antibodies, and a control area where anti-species immunoglobulin antibodies are fixed.  

6.2.3 Methods 

The testing method is based on immunochromatographic principles, in which antibodies labelled with colloidal 
particles (such as colloidal gold) react with target antigens to form a migrating antigen-antibody complex, which is 
captured by a second fixed antibody. A colour reaction takes place where the labelled particles are fixed.  

59 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

The tests can be used with positive liquid media tubes or visible colonies grown on solid media. In the case of 
liquid cultures, a 100 µl volume is dropped on to the test device. For solid cultures, 1 µl bacteria (=1 mm loop) or 1 
AFB+ colony (at least 1 mm) are re-suspended in the respective buffer, then vortexed and a 100 µl volume of 
these suspensions is used. The results should be read after 15 minutes but within 60 minutes of contact. 

6.2.4 Results/interpretation 

For a specific MPB64 antigen-antibody reaction, a red-purple colour band becomes visible within 15 minutes. The 
culture is interpreted as positive for M. tuberculosis complex if the colour reaction takes place in the test and 
control area. The intensities of the bands may vary. The specimen is interpreted as negative if a colour reaction 
takes place only in the control area. The test is invalid if no band is visible in the control area or if the background 
colour inhibits the test interpretation. Figure 7 gives examples of chromatographic immunoassays. 

Figure 7. Examples of chromatographic immunoassays for qualitative detection of M. tuberculosis 
complex 

Capilia TB-neo 

BD µGIT TBc identification test 

Developed with 100 µl of an AFB+ smear-positive liquid culture after 15 minutes incubation time. 

Although most M. tuberculosis complex strains may be correctly identified with the tests exhibiting a high 
sensitivity (92.4–99.2%) and specificity (100%), some test-negative strains have been isolated [2,3]. The reason 
for the failure of the test is the absence of MPB64 antigens in the culture medium, proven by the detection of a 
mutation in the MPB64 encoding mpb64 gene [3]. 

6.2.5 Biosafety 

Appropriate biosafety precautions for handling mycobacteria must be used. The dropping procedure, development, 
and reading of the test should be carried out in an appropriate biological safety cabinet in a BSL 3 laboratory. As 
used test devices may contain viable mycobacteria, they should be discarded safely according to institutional 
guidelines for handling BSL-3 material (see Chapter 1). 

6.3 Procedure 2: Line probe assay for the identification of 
the genus Mycobacterium and 16 different mycobacterial 
species including M. tuberculosis complex from culture 

Assays used: INNO-LiPA MYCOBACTERIA v2, Fujirebio Europe, Ghent, Belgium 

60 

 
 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

6.3.1 Introduction 

INNO-LiPA MYCOBACTERIA v2 is a line-probe assay for the simultaneous detection and identification of the genus 
Mycobacterium and 16 different mycobacterial species. The test is based on nucleotide differences in the 16S–23S 
rRNA spacer region and can be performed on either liquid or solid cultures [7,8]. 

6.3.2 Materials 

The materials required are a DNA thermal cycler, microtube centrifuge, water baths or heating blocks, a blotting 
device including a tray for the strips, a vortex, a rack, adjustable micropipettes, disposable pipette tips, 1.5 ml 
screw-top microcentrifuge tubes, gloves, thermostable DNA polymerase, autoclaved distilled water, TE buffer (10 
mM Tris-HCl, 1 mM EDTA, pH 8.0) and reagents from the kit (amplification buffer, primer mix, µgCl2 solution, 
reverse line blots, hybridisation solution, stringent wash solution, denaturation solution, conjugate solution, 
conjugate buffer, substrate solution and rinse buffer). 

6.3.3 Methods 

The test comprises three major parts: DNA extraction, DNA amplification and hybridisation. 

For DNA extraction from solid cultures, a loopful of bacteria is transferred and re-suspended in 0.5 ml TE buffer in 
a screw-top microcentrifuge tube. For liquid cultures, 500 µl of the liquid culture containing some bacterial clumps 
with as much bacteria as possible (e.g. taken from the bottom) are transferred directly to a screw-top 
microcentrifuge tube. All samples are boiled for ten minutes at a temperature of at least 95°C. After centrifugation 
at 17 900g for five minutes, 2 µl of the supernatant can be used for amplification.  

For amplification, the following mixture should be prepared:  

 
 
 
 
 
 

14.8 µl autoclaved distilled water 
10 µl amplification buffer 
10 µl primer mix 
10 µl µgCl2 solution 
0.2 µl Taq polymerase (1 U, 5U/µl) 
5 µl extracted DNA 

A negative control containing water instead of the extracted DNA must be prepared with every run of the test.  

The amplification profile is as follows: 

4 min 
95°C 
30 sec  95°C 
30 sec  62°C repeat steps 35 times 
30 sec  72°C 
End 

4°C 

If no automatic blotting system is used, hybridisation can be performed manually. For this purpose, 10 µl of the 
amplification product is added and carefully mixed with the denaturation solution in a disposable trough together 
with the test strip. Incubation time is five minutes at room temperature. After the addition of 2 ml pre-warmed 
hybridisation solution, the trough is shaken gently in a water bath at 62°C for 30 minutes. After removal of the 
hybridisation solution, the strips are washed with stringent wash solution twice at room temperature, and once at 
62°C for 10 minutes. The next two washing steps with rinse solution for one minute each are also at room 
temperature. The strips are then shaken for 30 minutes in the conjugate solution (streptavidin labelled with 
alkaline phosphatase). Washing of the test strip twice for one minute using rinse solution is followed by one 
washing step with substrate buffer. The test strip is then incubated in substrate solution for 30 minutes or until 
clearly visible bands develop. Colour development can be stopped by washing twice for three minutes with distilled 
water. After the strips have been dried on absorbent paper they can be interpreted. 

6.3.4 Results/interpretation 

The following Mycobacterium species can be detected simultaneously according to the interpretation scheme: M. 
tuberculosis complex, M. kansasii, M. xenopi, M. gordonae, M. genavense, M. simiae, M. marinum, M. ulcerans, M. 
celatum, MAIS, M. avium, M. intracellulare, M. scrofulaceum, M. malmoense, M. haemophilum, M. chelonae 
complex, M. fortuitum complex and M. smegmatis (Figure 8). 

61 

 
 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Figure 8. Interpretation scheme for INNO-LiPA 

Marker line 
1 - Conjugate control 
2 - Mycobacteria 
3 - MTBC 
4 - M. kansasii I 
5 - M. kansasii II 
6 - M. kansasii III, IV, V, M. gastri 
7 - M. xenopi 
8 - M. gordonae 
9 - M. genavense 
10- M. simiae 
11- M. marinum, M. ulcerans 
12- M. celatum 
13- MAIS complex 
14- M. avium  
15- M. intracellulare I 
16- M. intracellulare II 
17- M. scrofulaceum 
18- M. malmoense 
19- M haemophilum 
20- M. chelonae I-IV 
21- M. chelonae III 
22- M. chelonae I 
23- M. fortuitum complex 
24. M. smegmatis 

In one study [8], the overall specificity and sensitivity of the assay was estimated at 100% for the genus-specific 
probe. For the other probes, the sensitivity was 100%, while the total specificity was 92.2% or 94.4% depending 
on whether two specimens of very rare species (one M. thermoresistibile and one M. agri) were excluded from the 
study or not. Another group reported excellent sensitivity and specificity for all species and complexes for which 
the test is licensed [7]. 

6.3.5 Biosafety 

Appropriate biosafety precautions for handling mycobacteria have to be used. Screw-top Eppendorf tubes should 
be used throughout when heating mycobacteria. The transfer of bacteria in the tubes prior to and during boiling 
should be carried out in an appropriate biological safety cabinet in a BSL3 laboratory. After heating, further steps 
can be performed outside the safety cabinet. 

6.4 Procedure 3: Line probe assay for the identification of 
the M. tuberculosis complex and the detection of rifampicin 
resistance in M. tuberculosis 

Assay used: INNO-LiPA Rif. TB kit, Fujirebio Europe, Ghent, Belgium 

6.4.1 Introduction 

The LiPA rpoB PCR can be performed on all respiratory specimens and other specimens where the detection of 
rifampicin resistance in M. tuberculosis is the primary purpose of the investigation [6,Error! Reference source n
ot found.]. The PCR described is for use with all non-cerebral spinal fluid (CSF) specimens unless otherwise 
specified. 

6.4.2 Materials 

INNO-LiPA Rif.TB kit – Fujirebio Europe K1044.  

A full explanation of the principle, methodology and interpretation of the LiPA can be found in the instruction 
booklet included in each kit.  

Gloves and guarded tips should be used throughout the procedure. 
62 

 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

6.4.3 Methods 

Each PCR run should include: 

 
 
 
 
 
 

each sample in duplicate 
an inhibition control for each sample 
the decontaminated, extracted negative control 
five extracted negative controls (water) 
the decontaminated, extracted, positive control; and 
a positive control with a small amount of DNA. 

DNA extraction 
See Section 6.4.3 above. Ensure DNA extraction is carried out in a BSL3 laboratory. 

Amplification 
A one step amplification performed on DNA from culture though a nested PCR (higher sensitivity) is recommended on 
DNA extracted from specimens. 

To be carried out in a PCR clean room. A clean room is any laboratory area without mycobacterial DNA and PCR 
amplification products. Never bring PCR amplification products back into a clean area; this includes the laboratory 
scientist’s clothing, reagents, equipment, etc. unless thorough decontamination has been carried out to remove 
DNA/RNA. 

While samples are in the 80°C heating-block (see DNA extraction), prepare the PCR tubes. 

 

 

 

 

Remove enough 2X buffer (mix) and outer primers (LiPAOP1/2 2 pmol/µl) from the freezer and allow to 
thaw. 
Prepare the bulk PCR mix in a screw-cap microfuge tube. For each reaction required add: 

 
 
 
 

10 µl purified water 
20 µl 2X buffer 
10 µl primer mix 
0.2 µl Taq DNA polymerase 

Mix by inverting the tube 10 times, then briefly centrifuge before distributing 30 µl aliquots into labelled 0.2 
ml thin-wall PCR tubes. 
Close lids gently and transfer to the specimen preparation room. 

In the specimen preparation room: 

 
 

 

 

Place the PCR tubes in a PCR rack and place in a Class-1 cabinet. 
Using a clean guarded tip for each tube, add 10 µl of DNA extract or control to the appropriately labelled 
PCR tube. Once all extracts and controls have been transferred, add 1 µl of inhibition control to the 
inhibition control tubes. 
Close tubes tightly and transfer to the PCR product lab. Note: Remove coat and carry tubes using gloves. 
Do not take anything into the PCR product lab. 
Place tubes in the thermal cycler and close lid. The PCR cycles should be: 

15 min  95°C 
95°C 
60 s 
58°C  
30 s 
90 s 
72°C 
10 min  70°C 
End 

4°C 

repeat steps 35 times 

∞ 

The reaction should take about 2.5 hours (it is convenient to run this overnight). Shortly before the cycling is 
complete, prepare the second round reactions. 

Nesting the PCR reactions 
Preparing the second-round reactions. 

In the PCR clean room: 

 

 

Remove enough 2X buffer (mix) and inner primers (LiPAIP1/2 2 pmol/µl) from the freezer and allow to 
thaw. 
Prepare the bulk PCR mix in a screw-cap microfuge tube. For each reaction required add:  

 
 
 
 

10 µl purified water 
20 µl 2X buffer 
10 µl primer mix 
0.2 µl Taq DNA polymerase 

63 

 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 
 

Mix by inverting the tube 10 times and distribute 40 µl aliquots into labelled 0.2 ml thin-wall PCR tubes. 
Close lids gently and transfer to the PCR product lab.  

Nesting procedure 
 

When the first-round cycling is complete remove the tubes from the thermal cycler and place in the rack 
labelled ‘nesting’. Centrifuge the tubes in the picofuge for one minute.  
Assemble all the required equipment in the Template-Tamer workstation – the nesting pipette, the nesting 
tips, and the second-round reaction tubes. 
Change gloves directly before nesting. Add 1 µl of first-round reaction directly to the liquid in the 
appropriate second-round tube. Be careful not to touch the underside of the microfuge lid. 
Spin the tubes briefly in the picofuge and load onto the thermal cycler before closing the lid. 
Place tubes in the thermal cycler and close lid. The PCR cycles should be: 

 

 

 
 

15 min  95°C 
95°C 
30 s 
65°C 
30 s 
30 s 
72°C 
10 min  70°C 
End 

4°C 

repeat steps 35 times 

∞ 

Hybridisation 
In PCR product lab: 

Remove INNO-LiPA Rif.TB box from fridge. Preheat the hybridisation solution and stringent wash (SW) 
solution to 62°C. Allow other contents to warm up to room temperature while bath heats to 62°C. Check 
using a thermometer and adjust accordingly. Temperature must be  0.5°C for accurate results. 
Place required number of hybridisation trays in plastic rack. 
Mix the denaturation solution. Using a plugged 20 µl pipette tip and a P20 pipette, place 10 µl of 
denaturation solution into all trays to be used in the assay. 
Using a new 20 µl plugged pipette tip for each sample, add 10 µl of PCR product and mix (by pipetting up 
and down six times) with the denaturation solution in the appropriate tray. 
Allow the PCR product to denature for five minutes (important: DNA must be single-stranded for the 
hybridisation to work properly). 
Using forceps, remove the appropriate number of test strips and place on clean paper. Label the strips by 
marking them with a pencil above the red marker line. Avoid touching the strip below the red marker line as 
this can damage and remove the probes. 
Swirl the hybridisation solution to ensure all contents are dissolved. Using a P1000 pipette and a plugged 
pipette tip, place 1 ml of hybridisation solution in each tray. Mix briefly by rocking. Place a test strip in each 
tray and ensure that they are fully submerged. 
Place tray in the shaking bath and leave for 30 minutes. 
After 30 minutes remove the tray from the bath and place on absorbent paper. Remove the hybridisation 
solution using the tap vacuum to discard into the sink and add 1 ml of SW solution. Agitate gently for one 
minute. Repeat this wash step once. Remove solution and add 1 ml of SW solution. 
Place back in the shaking water bath for another ten minutes. 
While stringent wash is in progress make up the follow solutions: 
 

Rinse solution: dilute 1 in 5 with sterile distilled water. For each test, make 5 ml of the working 
strength solution. 
Conjugate: dilute 1 in 100 in conjugate diluent. Make up 1 ml for each test (if performing multiple 
tests consider making up one extra volume to give excess volume if required). To do this, for each 
test to be performed add 10 µl of conjugate concentrate and 990 µl of conjugate diluent to a plastic 
universal tube and mix. 

 

After 10 minutes of stringent wash remove the tray from the water bath and place on absorbent paper. 
Remove SW solution as above and add 1 ml of rinse solution and agitate for 1 minute. Repeat this wash 
step. Remove all the rinse solution and add 1 ml of conjugate solution. 
Leave agitating on the small orbital platform shaker at room temperature (20–25°C) for 30 minutes. 
Just before the end of this incubation step, prepare the colour substrate. To do this, dilute the substrate 
concentrate 1 in 100 with substrate buffer (i.e. for each test to be performed add 10 µl of substrate 
concentrate and 990 µl of substrate buffer into a plastic universal and mix.) 
Wash strips twice for a minute each in rinse solution as above. Wash strip for a further minute in 1 ml of 
substrate buffer. 

 

 

 

 

 

 

 

 
 

 
 

 

 
 

 

64 

 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

 

 
 
 

Add 1 ml of diluted substrate to each test and agitate at room temperature for 30 minutes (can be left 
longer if colour development is faint). 
Transfer strips to a tray containing 50 ml distilled water and leave for five minutes with occasional agitation. 
Remove strips and place on clean white paper; allow strips to dry before interpretation. 
Seal the dried strips under plastic tape on the appropriate request form for storage. 

6.4.4 Results/interpretation 

Products of c260bp in any of the negative controls must be analysed by LiPA. A LiPA-positive for M. tuberculosis 
complex in any of the negative controls invalidates the assay. 

No product in the low-positive control but positive-inhibition controls indicates a reduced sensitivity for the assay. 

Record the test as negative for M. tuberculosis complex if the duplicate PCRs are negative and the inhibition control 
is positive. The report should state: 

‘The molecular amplification test was negative for Mycobacterium tuberculosis complex. This does not exclude the 
diagnosis of tuberculosis.’ 

If both duplicates are PCR-positive (c260bp), one duplicate is analysed by LiPA. A guide to the interpretation of the 
LiPA is given in Figure 9. 

A wild-type genotype contains no mutations. Genotypes other than wild type are mutant genotypes. 

If the LiPA is negative for M. tuberculosis complex, the test is negative for M. tuberculosis complex and the report 
should state:  

‘The molecular amplification test was negative for Mycobacterium tuberculosis complex. This does not exclude the 
diagnosis of tuberculosis.’ 

If the LiPA is positive for M. tuberculosis complex and has a wild-type genotype, the M. tuberculosis complex is 
likely to be rifampicin-sensitive and the report should read: 

‘The performed test indicated: 

 
 

the presence of Mycobacterium tuberculosis complex 
the region coding for the B-subunit of the RNA polymerase contained no mutations associated with 
rifampicin resistance. 

Note: This test is unable to detect true rifampicin resistance in a small percentage of isolates. 

If the LiPA is positive for M. tuberculosis complex and has a mutant genotype, the M. tuberculosis complex is likely 
to be rifampicin resistant and the report should read: 

‘The performed test indicated: 

 
 

the presence of Mycobacterium tuberculosis complex 
there were mutations in the rpoB gene which would confer rifampicin resistance. 

If one duplicate is PCR-positive, this should be analysed by the LiPA. If the LiPA is negative for M. tuberculosis 
complex, record the test as negative for M. tuberculosis complex (see above). If positive for M. tuberculosis 
complex the test is inconclusive and the PCR must be repeated in duplicate from the extracts. If the repeat results 
are still discordant then the report should read: 

 

‘The PCR was performed in duplicate on two separate occasions. On each occasion only one duplicate was 
positive for Mycobacterium tuberculosis complex. This sample is likely to be positive for Mycobacterium 
tuberculosis complex with no mutations for rifampicin resistance. If possible, please send a repeat sample 
for confirmation.’ 

65 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Figure 9. Interpretation of LiPA 

S3 

S4 

MtbC  

S2 

R4a 

R4b 

R2 

Conjugate 

S1 

S5 

R5 

If the repeat results are both negative, then the report should read: 

‘Unfortunately, the PCR was equivocal. If possible, please send another sample for testing.  
Note: It will not be possible to repeat the PCR on CSF samples and the result on these samples should be recorded 
as inconclusive.’ 

If the inhibition control is PCR-negative but the sample is PCR-positive in duplicate, then analyse the product by 
LiPA and record the result as above. 

If the inhibition control and the duplicate tests are PCR negative, the PCR is repeated in duplicate from the extract. 
It will not be possible to repeat the PCR on CSF samples. If the inhibition control is still PCR negative, then record 
the test as inhibited. The report should read: 

‘The PCR was negative although the results suggest the presence of PCR inhibitors.’ 

The following note should be added to reports on the analysis of paraffin-wax-embedded blocks: 

‘The sensitivity of this assay may be severely reduced when performed on paraffin-wax-embedded tissue. A more 
appropriate specimen for the detection of Mycobacterium tuberculosis would be unfixed material.’ 

66 

MtbCrpoBR5/S531L (RIF resistant)MtbCrpoBwild type (RIF sensitive)MtbC not detectedMtbCrpoBDS1 (RIF resistant)MtbCrpoBDS2 (RIF resistant)MtbCrpoBDS3 (RIF resistant)MtbCrpoBDS4 (RIF resistant)MtbCrpoBR4a/H526Y (RIF resistant)MtbCrpoBR4b/H526D (RIF resistant)MtbCrpoBDS5 (RIF resistant)MtbCrpoBR2/D516V (RIF resistant) 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

6.5 Procedure 4: Line probe assay for identifying species 
from Mycobacterium genus and detecting potential 
multidrug and extensively multidrug-resistant tuberculosis 
(MDR- and XDR-TB) from cultures and smear-positive 
specimens 

Assays used: Hain Lifescience GenoType CM, AS and M. tuberculosis complex tests and Hain Lifescience GenoType 
MTBDRplus and MTBDRsl 

6.5.1 Introduction 

The GenoType series is based on DNA strip technology and allows for the genetic differentiation of species belonging 
to the genus Mycobacteria. The Hain CM test is used to identify common mycobacteria and the AS test to further 
differentiate additional species. The GenoType MTBC test differentiates between the species of the M. tuberculosis 
complex. The CM, AS and MTBC strips detect and analyse positive mycobacterial cultures and must not be used to 
detect mycobacteria directly from patient material. 

The GenoType MTBDRplus test allows for the detection of M. tuberculosis complex and simultaneously its resistance 
to rifampicin and/or isoniazid by mutations in the rpoB and katG/inhA (high/low isoniazid resistance) genes, 
respectively [9]. The GenoType MTBDRsl simultaneously detects M. tuberculosis complex and its resistance to 
fluoroquinolones (e.g. ofloxacin and moxifloxacin) and/or aminoglycosides/cyclic peptides (injectable antibiotics as 
capreomycin, viomycin/kanamycin, amikacin) and/or ethambutol. The MTBDRplus and MTBDRsl are validated for DNA 
extracted from both positive cultures and smear-positive pulmonary specimens. Note: these tests should not be used 
to detect mycobacteria directly from smear-negative materials unless the laboratory independently validates their use. 
They are licensed for smear-positive sputum only. The currently available GenoType MTBDRplus v.2 assay has better 
sensitivity characteristics. 

All procedures are identical and are divided into three steps: DNA extraction, a multiplex amplification using 
biotinylated primers, and reverse hybridisation. 

6.5.2 Materials 

The GenoType series all use the same reagents except for the primer/nucleotide/dye mix (PNM), which is specific 
to each test kit. 

Materials required and provided by the manufacturer 

Ready to use: 

 
 
 
 
 
 
 

PNM (primer/nucleotide/dye mix). Note: different PNM for each test kit; or 
AM-A and AM-B mixes (GenoType MTBDRplus v.2 only) 
Denaturing solution (contains <2% NaOH, irritating to eyes and skin) 
Hybridisation solution (contains 8–10% anionic) 
Stringent wash solution (contains >25% quaternary ammonium compound, <1% anionic) 
Rinse solution (contains buffer, <1% NaCl, <1% anionic) 
Nitrocellulose membranes. 

Prepare for use: 

 

 

Conjugate (contains streptavidin-conjugated alkaline phosphatase): Calculate how many tests are being 
performed (+3) and add concentrate (CON-C) to diluent (CON-D) in the proportions of 10 µl CON-C to 1 ml 
CON-D per test. Note: this must be made fresh each time. 
Substrate containing dimethyl sulphoxide (irritant): Add the contents of the substrate concentrate (SUB-C) 
to the contents of the substrate diluent (SUB-D). Once made, the solution can be kept for four weeks at 
room temperature, provided it is protected from light – it must be stored in the brown SUB-D bottle. 

Materials required not provided by the manufacturer 
 
 
 
 
 
 
 
 
 

Absorbent paper 
Adjustable pipettes and disposable tips 
DNA extraction reagents 
PCR tubes (DNase and RNase free) 
Shaking water bath/TwinCubator 
Shaking platform/TwinCubator 
Thermal cycler 
Thermostable DNA polymerase with buffer (hot-start enzyme recommended) 
Thin-walled PCR tubes 

67 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 
 
 

Tweezers 
Ultrasonic bath 
Water (molecular biology grade). 

6.5.3 Methods 

DNA extraction 
DNA extraction must be carried out in a BSL3 laboratory in a biological safety cabinet. 

 

 

 

 

DNA extraction from solid cultures: Using a 1 µl loop, transfer a small amount of growth to a 1.5 ml screw-
top Eppendorf tube containing 100 µl molecular-grade water. 
DNA extraction from liquid cultures and primary specimens: For very large volumes of culture (over 2 ml) 
centrifuge at 3000g for 20 minutes and discard the supernatant, leaving about 1 ml. Re-suspend the 
deposit in the remaining fluid and add 100 µl to a 1.5 ml screw-top Eppendorf tube. Note: Primary 
specimens should not be used with AS and CM strips. For smear-positive sputum specimens, centrifuge 
500 µl of decontaminated sample (see NALC-NaOH decontamination – see Section 5.4.1) as above and re-
suspend in 100 µl molecular-grade water in a 1.5 ml screw-top centrifuge tube. Add 100 µl to a 1.5 ml 
screw-top centrifuge tube; if there is a very small volume, make up to 0.25 ml with sterile Middlebrook. 
Alternatively, GenoLyse kit (Hain Lifescience) could be used for the DNA extraction from cultures and 
primary specimens. 
Treatment of blood and bone marrow cultures or cultures containing pus or blood prior to Hain genotyping 
is not validated by Hain and therefore only an alternative method. Excessive cellular matter can have an 
inhibitory action on polymerase chain reactions (PCRs) and therefore, it is necessary to treat those samples 
prior to DNA extraction: 

 
 
 
 
 
 
 
 

Pipette 0.5 of the culture into a plastic universal. 
Add 0.25 ml Triton X and 0.25 ml 1N NaOH. 
Vortex. 
Add 9 ml sterile distilled water and vortex again. 
Centrifuge at 3000g for 20 minutes. 
In the cabinet, pour off all the supernatant into another universal and discard. 
Re-suspend the pellet by adding 0.25 ml sterile Middlebrook medium and vortexing. 
Add 100 µl of this deposit to a 1.5 ml screw-top centrifuge tube. 

For the negative control: Add 100 µl of molecular water to a 1.5 ml centrifuge tube. Negative controls must be 
prepared and included in every run of the test. 

All tubes: 

 
 

Add 100 µl chloroform and vortex. 
Place in a covered water bath at 80°C for at least 30 minutes. 

At this stage the Mycobacterium spp. are inactivated by heating or chloroform treatment and can be considered 
safe. Processing can therefore continue outside the BSL3 laboratory. 

 
 

Place the microcentrifuge tube at –20°C for 10 minutes. 
After 10 minutes take samples out of freezer and allow to thaw whilst preparing the PCR mix. 

PCR amplification 
To be prepared in a clean room. A clean room is any laboratory area without DNA and PCR amplification products. 
Never bring PCR amplification products into a clean area; this includes laboratory workers’ clothing, reagents, 
equipment, etc. unless thorough decontamination has been carried out to remove DNA/RNA. 

PCR reaction mix 
Make up PCR reaction mix: 

 
 
 
 
 
 

35 µl PNM mix (remember to use the correct kit PNM for the test performed) 
5 µl PCR buffer 
2 µl magnesium chloride final concentration 2.5 mM 
2.8 µl molecular water (Sigma) 
0.2 µl (1U) Hot-start Taq 
Total 45 µl 

Pipette 45 µl into a 0.2 ml x 8-strip thin-wall tube (+ individual caps) as required. It may be helpful to use a 
different-coloured tube for each day of the week to help minimise contamination of the products. 

For GenoType MTBDRplus v.2 assay, mix the following (please note: ready-made mixes AM-A and AM-B contain Taq 
polymerase): 

10 µl AM-A 

 

68 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

 
 

35 µl AM-B 
5 µl extracted DNA 

(Please refer to the Operator’s manual for detailed instructions). 

Amplification 
This procedure should be conducted in the DNA-specimen preparation room.  

 
 
 

 

 

Centrifuge thawed samples (DNA preparation) at 13000g for three minutes. 
Label 0.2 ml x 8-strip thin-wall tubes with the corresponding worksheet number (1 to N).  
After centrifugation carefully pipette 5 µl of the top aqueous solution to the appropriate tube with PCR mix 
and seal the cap. Carry on until all have been pipetted.  
Place the 0.2 ml x 8-strip thin-wall tube (+ individual caps) into a diagnostic thermocycler, close the lid and 
screw tight. 
Run the amplification cycle: 

15 min  95°C 
95°C 
30 s 
2 min 
58°C 
25 sec  95°C 
40 sec  53°C  
40 sec  70°C 
70°C 
8 min 
4°C 
End 

repeat steps 10 times 

repeat steps 20 times 

∞ 

The reaction time is approximately 1 hour and 50 minutes. 

Hybridisation of PCR amplicon onto the Hain strips3 
Hybridisation can either be done automatically, for example with a Bee Blot machine, or manually, using a 
TwinCubator machine. Always wear gloves when handling the strips. 

Preparation: 

 

 

 

 
 

 

 

 
 
 

 
 

 

Pre-warm shaking water bath/TwinCubator to 45°C. Prewarm HYB and STR solutions to 37–45°C before 
use.  
The reagents must be free from precipitates (note, however, that solution CON-D is opaque). Mix if 
necessary. 
Warm the remaining reagents (with the exception of CON-C and SUB-C) to room temperature. Using a 
suitable tube, dilute conjugate concentrate (CON-C, orange) and substrate concentrate (SUB-C, yellow) 
1:100 with the respective buffer (CON-C with CON-D, SUB-C with SUB-D) in the amounts needed. Mix well 
and bring to room temperature. For each strip, add 10 µl concentrate to 1 ml of the respective buffer. 
Dilute CON-C before each use. Diluted SUB-C is stable for four weeks if stored at room temperature and 
protected from light. 
Dispense 20 µl of denaturation solution (DEN, blue) in a corner of each of the wells used. 
Add 20 µl of amplified sample to the solution, pipette up and down to mix well and incubate at room 
temperature for five minutes.  
Meanwhile, take the strips out of the container using tweezers and mark them with a pencil underneath the 
marker line. Always wear gloves when handling strips. 
Carefully add 1 ml of pre-warmed hybridisation buffer (HYB, green) to each well. Gently shake the tray until 
the solution has a homogenous colour.  
Take care not to spill the solution into the neighbouring wells.  
Place a strip in each well.  
The strips must be completely covered by the solution and the coated side (identifiable by the marker line 
near the lower end) must face upward. Using pipette tips, turn over strips which may have turned when 
immersed in the solution. Carefully clean tweezers under warm running water and dry after each use to 
avoid contamination. (These measures also apply to all subsequent steps.) 
Alternatively, place tray in TwinCubator and incubate for 30 minutes at 45°C. 
Adjust the shaking frequency of the water bath to achieve a constant and thorough mixing of the solution. 
To allow adequate heat transfer, the tray must be dipped into the water to at least one third of its height.  
Completely aspirate the hybridisation buffer using, for example, a Pasteur pipette connected to a vacuum 
pump. 

3 Descriptions of laboratory procedures are based on the manufacturer’s instructions (Hain Lifescience). 
The original text is available from: http://www.tbevidence.org/documents/rescentre/sop/MTBDRsl.pdf. 

69 

 
 
 
 
 
                                                                    
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 

 
 
 

 

 

 

 
 

 

 
 

Add 1 ml of stringent wash solution (STR, red) to each strip and incubate for 15 minutes at 45°C in shaking 
water bath/TwinCubator. 
Work at room temperature from this step forward. 
Completely remove the stringent wash solution.  
Pour out wash solution in a waste container and remove all remaining fluid by turning the tray upside down 
and gently tapping it on absorbent blotting paper. (This also applies to all other wash steps.) 
Wash each strip once with 1 ml of rinse solution (RIN) for one minute on shaking platform/TwinCubator 
(pour out RIN after incubation). 
Add 1 ml of diluted conjugate (see above) to each strip and incubate for 30 minutes on a shaking 
platform/TwinCubator (pour out RIN after incubation).  
Remove the solution and wash each strip twice for one minute with 1 ml of rinse solution (RIN) and once 
for 1 minute with approximately 1 ml of distilled water (e.g. use wash bottle) on a shaking 
platform/TwinCubator (pour out solution each time). 
Ensure all traces of water are removed after the last wash.  
Add 1 ml of diluted substrate (see above) to each strip and incubate (protected from light) without shaking 
for ten minutes. 
Depending on the test conditions (e.g. room temperature), the substrate incubation time can vary from 
three to 20 minutes. Extended substrate incubation times can lead to increased background staining and 
might impair interpretation of the results. 
Stop the reaction by briefly rinsing twice with distilled water. 
Using tweezers, remove the strips from the tray and dry them between two layers of absorbent blotting 
paper.  

6.5.4 Results/interpretation 

Interpretation rules are available in the manufacturer’s inserts (Figures 10–14). 

Figure 10. Interpretation sheet for GenoType Mycobacterium CM 

70 

 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Figure 11. Interpretation sheet for GenoType Mycobacterium AS 

Figure 12. Interpretation sheet for GenoType Mycobacterium MTBC 

71 

 
 
 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Figure 13. Interpretation sheet for GenoType Mycobacterium MTBDRplus 

Figure 14. Interpretation sheet for GenoType Mycobacterium MTBDRsl 

72 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

To validate a run in any of these systems, all negative controls must be negative, and positive controls must give 
the wild-type hybridisation pattern shown on all strips (Figures 6.4 to 6.8). Thus, a line must develop in the 
conjugate control (CC) zone and in the universal control (UC) zone, which detects all known mycobacteria and 
members of the group of gram-positive bacteria with a high G+C content. Furthermore, banding in the MTBC/TUB 
region indicates amplicons are generated from M. tuberculosis complex members. 

No hybridisation or poor hybridisation with a low positive control but a positive amplification control indicates a 
reduced sensitivity for the assay. 

6.5.5 Examples of reporting for GenoType Mycobacterium MTBDRplus 

Record the test as negative for M. tuberculosis complex if only the conjugate control and AC are positive. The 
report should state: 

 
 

‘The PCR test was negative for Mycobacterium tuberculosis complex. 
This does not exclude the diagnosis of tuberculosis.’ 

If the MTBDRplus strip is positive for M. tuberculosis complex and has a wild type rpoB, katG and inhA, as in strip 1 
(Figure 13), the M. tuberculosis complex is likely to be rifampicin-sensitive and the report should read: 

‘The performed test indicated: 

 
 

the presence of Mycobacterium tuberculosis complex; and 
the region coding for the β-subunit of the RNA polymerase contained no mutations associated with 
rifampicin resistance. 

Note: Detection of non rpoB mutation does not rule out rifampicin resistance as the test is unable to detect true 
rifampicin resistance in a small percentage of isolates (not all rifampicin-resistance-associated mutations are 
covered).’ 

If the MTBDRplus strip is positive for M. tuberculosis complex and has a mutant rpoB but wild type katG and inhA, 
the M. tuberculosis complex is likely rifampicin-resistant and the report should read: 

‘The performed test indicated: 

 
 

the presence of Mycobacterium tuberculosis complex; and 
there were mutations in the rpoB gene which would confer rifampicin resistance’. 

If the MTBDRplus strip is positive for M. tuberculosis complex and has a wild type rpoB but mutant katG and/or 
inhA (e.g. strip 3, Figure 13), the M. tuberculosis complex is likely isoniazid-resistant and the report should read: 

‘The performed test indicated: 

 
 

 

the presence of Mycobacterium tuberculosis complex; and 
the region coding for the β-subunit of the RNA polymerase contained no mutations associated with 
rifampicin resistance. 
There was a mutation in katG/inhA that is usually seen in isoniazid resistant isolates. 

Note: This test is unable to detect true rifampicin resistance in a small percentage of isolates.’ 

If the M. tuberculosis complex probe is negative but multiple locus control probes are visible or the M. tuberculosis 
complex probe is positive alone, report as equivocal. The report should read: 

 

‘The PCR test gave an equivocal result.’ 

If the amplification control and the test is negative, the PCR is repeated from the extract at 1/10 dilution in water. 
If the inhibition control is still negative then record the test as inhibited. The report should read: 

 

‘The PCR was negative but the results suggest the presence of PCR inhibitors which could give a false 
negative result.’ 

6.5.6 Biosafety 

Appropriate biosafety precautions must be taken when handling mycobacteria. The transfer of bacteria to tubes 
and the addition of chloroform and boiling during DNA preparation should be carried out in an appropriate safety 
cabinet in a BSL3 laboratory. After microorganisms are inactivated by heating or chloroform treatment, the process 
can be continued outside the BSL3. 

73 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

6.6 Procedure 5: Nucleic acid hybridisation test for the 
identification of M. tuberculosis complex 

Assay used: AccuProbe Mycobacterium tuberculosis Complex Culture Identification Test Kit, Gen-Probe 
Incorporated, San Diego, CA, USA. 

6.6.1 Introduction 

Fast species identification of a clinical isolate is important for rapid diagnosis. With a nucleic acid hybridisation test 
[1], members of the MTB complex can be identified within less than an hour [4,5]. The test does not react to non-
tuberculous mycobacteria and does not differentiate between members of the M. tuberculosis complex, but the 
result of M. tuberculosis complex is sufficient for most clinical laboratories since M. tuberculosis is the most 
prevalent of the M. tuberculosis complex organisms. 

6.6.2 Materials 

An illuminometer, sonicator, water bath or heating block, rack, adjustable micropipettes, gloves, vortex, and 
reagents from the kit are required [1]. 

6.6.3 Methods 

The test uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal 
RNA of the target. After the ribosomal RNA of the bacteria is released, the labelled DNA probe combines with the 
target RNA to form a stable DNA:RNA hybrid, which can be measured in a illuminometer. The decision to test a 
culture with an MTB complex probe may also depend on the appearance under the microscope (in liquid medium) 
and the pigmentation of the bacteria or the pellet. 

For solid cultures, 100 µl of reagent 1 (lysis reagent) and 100 µl of reagent 2 (hybridisation buffer) are transferred 
into a reagent tube. For liquid cultures, only 100 µl of reagent 2 is needed. Samples (a loopful of bacteria or 100 µl 
of a mixed culture suspension) are added and mixed well by vortexing. 

The tubes are incubated for 15 minutes in the sonication bath and subsequently for ten minutes at 95°C. A 100 µl 
volume of the lysed specimens is transferred into probe containing tubes, which are incubated for 15 minutes at 
59.5–61°C (exact time and temperature is critical). 

For the visualisation of the hybridisation product, 300 µl of the selection reagent are added, mixed well by 
vortexing, and again incubated for ten minutes at 59.5–61°C (exact time and temperature is critical). The samples 
can be analysed in an illuminometer after having cooled off to room temperature (one hour). The whole procedure 
can be completed within one hour. 

6.6.4 Results/interpretation 

The results of the tests are based on cut-off values. Samples producing signals greater than or equal to these cut-
off values are considered positive, results below these cut-off values are considered negative; intermediate results 
should be repeated. The cut-off values are device-specific. 

The result is only valid if the included negative (e.g. M. avium ATCC 25291) and positive (e.g. M. tuberculosis ATCC 
25177) controls are within a specified range of values. If the initial test gives a negative result, additional probes 
have to be performed. 

The non-radioactive DNA probes for the identification of M. tuberculosis complex were evaluated with 134 clinical 
isolates, which included 36 MTB complex isolates. Sensitivity and specificity was 100% [4]. Another study 
investigated 359 liquid vials positive for acid-fast bacilli, including 224 MTB complex isolates, and found an initial 
sensitivity of 87.2% for MTB complex [5]. 

A principle limitation of the probe technology is the inability to identify mixed cultures. If a mixed culture is 
suspected, additional probes might yield a result. However, only a limited number of species are covered by these 
additional probes. 

6.6.5 Biosafety 

Appropriate biosafety precautions for handling mycobacteria have to be used. The transfer of bacteria to the tubes 
for sonication and heating should be carried out in a BSL3 laboratory in an appropriate biosafety cabinet. After 
heating, the next steps can be performed outside the biosafety cabinet. 

74 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

6.7 Procedure 6: Single-use sample-processing cartridge 
system with integrated multicolour real-time PCR capacity 
for detection, identification of M. tuberculosis complex 
bacteria and detection of rifampicin resistance 

Assay used: The Xpert MTB/RIF and Xpert MTB/RIF Ultra assay with the Cepheid GeneXpert System, Cepheid, 
Sunnyvale, CA 

6.7.1 Introduction 

The culture methods for isolation of mycobacteria and the molecular methods for detection and/or characterisation 
of mycobacteria require specific infrastructure and well trained staff, which may limit the availability of these 
technologies to specialised laboratories [10]. The Xpert MTB/RIF assay overcomes these problems by providing 
rapid laboratory diagnosis of TB disease and prediction of resistance to rifampicin by a cartridge-based system 
using both processed and unprocessed clinical specimens. Xpert MTB/RIF showed high overall sensitivity with 
smear-positive/culture-positive TB samples (98%), but sensitivity is less optimal particularly in smear-
negative/culture-positive TB (68%) and HIV-co-infected TB patients (79%) [11]. 

The new version of the fully automated nested real-time PCR assay, Xpert MTB/RIF Ultra (Ultra), addressed the 
limitations in sensitivity of the Xpert MTB/RIF assay [12]. Ultra’s performance has been recently evaluated in a 
multicentre non-inferiority study, confirming an increase in sensitivity compared with the Xpert MTB/Rif assay by 
5% in smear-positive respiratory samples and 12% in smear-negative respiratory samples [12]. The main 
advantages of Ultra are the increased volume of processed specimens introduced to the PCR reaction, a faster PCR 
program and the more adequate target genes for detection of MTB (two multicopy genes IS6110 and IS 1081) 
[13]. In addition, rifampicin resistance is detected by the melting curve temperature-based analysis [13]. 

6.7.2 Materials 

Both Xpert MTB/RIF and Ultra require a specific hardware platform, as well as test kits, disposable pipettes, and 
gloves. 

The platform integrates sample processing, PCR and subsequent analysis of the PCR fragment. 

6.7.3 Methods 

The Xpert MTB/RIF and Ultra are based on a disposable plastic cartridge containing all reagents required for 
bacterial lysis, nucleic acid extraction, amplification, and amplicon detection. The only manual step is the addition 
of a bactericidal lysis buffer to sputum or decontaminated sputum. 

The lysis buffer is added in a 2:1 ratio (v/v) to untreated sputum of > 1 ml volume and in a 3:1 ratio to 
decontaminated sputum pellets > 0.5 ml volume. The additional buffer in decontaminated pellets is necessary in 
order to meet the assay minimum sample volume requirement. The closed sputum cup or centrifuge tube is 
incubated at room temperature for 15 minutes, during which time the samples must be manually agitated twice. 
Following this, 2 ml of the inactivated sample mixture are transferred to the cartridge (equivalent to 0.7 ml 
untreated sputum or 0.5 ml decontaminated pellet). Cartridges are then inserted into the platform and the 
programme is started. The duration of the run is 1 h 40 min on Xpert MTB/RIF; while 1 h 17 min for TB positive 
samples and 1 h 4 min for TB negative samples on Ultra. 

6.7.4 Results/Interpretation 

In both tests, results indicate the presence or absence of M. tuberculosis complex DNA with a semi-quantitative 
estimate of bacillary load, and the presence or absence of the most common mutations causing RIF resistance. 

On Xpert MTB/RIF, four semi-quantitative categories are used when the test detects MTBC (i.e. High, Medium, Low 
and Very Low). 

On Ultra, in addition the semi-quantitative categories of Xpert MTB/RIF, the “Trace” as a new semi-quantitative 
category has been introduced that corresponds to the lowest bacillary load for MTBC detection. 

The interpretation of trace results is as follows [12]: 

 

 

Among persons with HIV, children and extrapulmonary specimens “Trace calls” should be considered as 
true positive results for use in clinical decisions and patient follow-up. 
Among persons not at risk for HIV, with an initial “Trace” positive result, a fresh specimen from the patient 
should undergo repeat testing and the result of the second Ultra test be used for clinical decisions and 
patient follow-up. 

75 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

 

 

While clinical and available radiological information should always be considered in the diagnosis of 
tuberculosis, a second “Trace call” positive is sufficient to make a diagnosis of pulmonary TB unless there is 
a recent history of TB. 
Among people that test “Trace call” positive, additional investigations should be performed to confirm or 
exclude resistance to rifampicin. 

In both tests, three non-interpretable results are used (Invalid, Error and No Result). 

In both tests, three categories are used to determine RIF resistance (Rif resistance DETECTED, Rif resistance NOT 
DETECTED, or Rif resistance INDETERMINATE): 

 

 
 

Rif resistance DETECTED: mutation(s) within the 81 bp RRDR (Rifampicin Resistance Determining Region) 
detected 
Rif resistance NOT DETECTED: no mutation(s) within the 81 bp RRDR detected; and 
Rif resistance INDETERMINATE: the MTBC concentration was very low and resistance could not be 
determined. 

Interpretation of Rifampicin results for Xpert MTB/RIF and Ultra [14]: 

 

 

-  Rif resistance NOT DETECTED: RIF-resistant TB can be ruled out in most cases unless there is still a 
strong suspicion of drug resistance that may warrant further investigation. 
-  Rif resistance DETECTED: If the patient is at high risk of MDR-TB an MDR-TB treatment regimen should 
be initiated. If the patient is at low risk of MDR-TB, further confirmatory tests (such as a phenotypic DST, 
LPA, or sequencing) are required prior to initiation of treatment. 

The Xpert MTB/RIF and Ultra tests cannot be used for follow-up testing (monitoring) of patients on treatment, as 
they detect both live and dead bacteria. Interpretation of “very low” and “trace” results in patients with previous 
TB may require further clinical assessment and additional tools to exclude a false-positive result [15,16]. 

6.7.5 Biosafety 

Appropriate biosafety precautions for handling mycobacteria must be used. Biosafety precautions required for Xpert 
MTB/RIF are similar to those for smear microscopy with adequate space and ventilation [17]. After adding the lysis 
buffer, a marked reduction of viable bacteria occurs. The filled cartridges should not be opened again or 
manipulated. They should be discarded according to institutional guidelines. 

76 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

Abe C, Hirano K, Tomiyama T. Simple and Rapid Identification of the Mycobacterium tuberculosis Complex 
by Immunochromatographic Assay using Anti-MPB64 Monoclonal Antibodies. J Clin Microbiol. 1999 
Nov;37(11):3693-7. 

Hillemann D, Rüsch-Gerdes S, Richter E. Application of the Capilia TB assay for culture confirmation of 
Mycobacterium tuberculosis complex isolates. Int J Tuberc Lung Dis. 2005 Dec;9(12):1409-11. 

Hirano K, Aono A, Takahashi M, Abe C. Mutations Including IS6110 Insertion in the Gene Encoding the 
MPB64 Protein of Capilia TB-Negative Mycobacterium tuberculosis Isolates. J Clin Microbiol. 2004 
Jan;42(1):390-2. 

Lebrun L, Espinasse F, Poveda JD, Vincent-Levy-Frebault V. Evaluation of non-radioactive DNA probes for 
identification of mycobacteria. J Clin Microbiol. 1992 Oct;30(9):2476-2478. 

Reisner BS, Gatson AM, Woods GL. Use of Gen-Probe AccuProbes to identify Mycobacterium avium complex, 
Mycobacterium tuberculosis complex, Mycobacterium kansasii, and Mycobacterium gordonae directly from 
BACTEC TB broth cultures. J Clin Microbiol. 1994 Dec;32(12):2995-2998. 

Sam IC, Drobniewski F, More P, Kemp M, Brown T. Mycobacterium tuberculosis and Rifampin Resistance, 
United Kingdom. Emerg Infect Dis. 2006 May;12(5):752-9. 

Scarparo C, Piccoli P, Rigon A, Ruggiero G, Nista D, Piersimoni C. Direct Identification of Mycobacteria from 
MB/BacT Alert 3D bottles: Comparative Evaluation of Two Commercial Probe Assays. J Clin Microbiol. 2001 
Sep;39(9):3222-3227. 

Tortoli E, Mariottini A, Mazzarelli G. Evaluation of INNO-LiPA MYCOBACTERIA v2: Improved Reverse 
Hybridization Multiple DNA Probe Assay for Mycobacterial Identification. J Clin Microbiol. 2003 
Sep;41(9):4418-4420. 

Nikolayevskyy V, Balabanova Y, Simak T, Malomanova N, Fedorin I, Drobniewski F. Performance of the 
GenoType MTBDRPlus assay in the diagnosis of tuberculosis and drug resistance in Samara, Russian 
Federation. BMC Clin Pathol. 2009 Mar 10;9:2. 

10. 

Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S, Krapp F, et al. Rapid molecular detection of 
tuberculosis and rifampin resistance. N Engl J Med. 2010 Sep 9;363(11):1005-15. 

11.  World Health Organization. Automated real-time nucleic acid amplification technology for rapid and 

simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF assay for the diagnosis of 
pulmonary and extrapulmonary TB in adults and children. Policy update. Geneva: WHO; 2013. 

12.  World Health Organization. WHO Meeting Report of a Technical Expert Consultation: Non-inferiority analysis 

of Xpert MTB/RIF Ultra compared to Xpert MTB/RIF. Geneva, WHO; 2017. 

13. 

Chakravorty S, Simmons AM, Rowneki M, Parmar H, Cao Y, Ryan J, et al. The New Xpert MTB/RIF Ultra: 
Improving Detection of Mycobacterium tuberculosis and Resistance to Rifampin in an Assay Suitable for 
Point-of-Care Testing. MBio. 2017 Aug 29;8(4). 

14.  World Health Organization. Xpert MTB/RIF implementation manual - Technical and operational ‘how-to’: 

practical considerations. Geneva: WHO; 2014. 

15. 

16. 

Theron G, Venter R, Smith L, Esmail A, Randall P, Sood V, et al. False-Positive Xpert MTB/RIF Results in 
Retested Patients with Previous Tuberculosis: Frequency, Profile, and Prospective Clinical Outcomes. J Clin 
Microbiol. 2018 Feb 22;56(3). 

Bahr NC, Nuwagira E, Evans EE, Cresswell FV, Bystrom PV, Byamukama A, et al. Diagnostic accuracy of 
Xpert MTB/RIF Ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study. Lancet 
Infect Dis 2018 Jan;18(1):68-75. 

17.  World Health Organization. Tuberculosis Laboratory Biosafety Manual. Geneva, WHO; 2012. 

77 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

7. First- and second-line drug susceptibility 
testing for Mycobacterium tuberculosis 
complex 

Emmanuelle Cambau, Sabine Rüsch-Gerdes 

Revised by Emmanuelle Cambau (2015) 

7.1 Background and principles 

This chapter describes the susceptibility testing for Mycobacterium tuberculosis and other members of the M. 
tuberculosis complex (MTBC; M. africanum, and M. bovis being the most common) to anti-tuberculous drugs [11]. 

Major objectives for drug susceptibility testing (DST) in tuberculosis include: (i) ensuring effective individual 
treatment and management of a tuberculosis case, (ii) anti-tuberculosis drug resistance surveillance at the level of 
a hospital, city, region or country; (iii) identification of the need for institutional isolation of patients; and (iv) 
determination of the scope of institutional and community outbreak investigations required [13]. Because of the 
development of drug resistance in tuberculosis worldwide, drug susceptibility testing to first-line drugs is required 
for a definite case of tuberculosis (a patient with a positive culture for the M. tuberculosis complex or one sputum 
smear positive for acid-fast bacilli if a culture is not available). Drug resistance rates are higher in re-treatment 
cases (acquired resistance or secondary resistance) than in new cases (primary resistance), the difference varying 
according to the country or epidemiological situation [11]. Drug resistance during treatment, designated as 
‘acquired’ or ‘secondary resistance’, results from the selection and multiplication of resistant mutant isolates pre-
existing in the tubercle bacillus population before therapy. Drug resistance observed before treatment, designated 
as ‘primary resistance’, is the consequence of exposure to a drug-resistant source of infection [14,16,22]. 

Drug susceptibility testing to second-line drugs is mandatory for multidrug-resistant cases of TB (MDR-TB) – i.e. 
those resistant to at least rifampicin and isoniazid – and for patients who have previously been treated for 
tuberculosis with second-line drugs. Drug susceptibility testing should be repeated for a definite case if the culture 
is still positive after five months of treatment. It may also be repeated after three months of treatment if sufficient 
funds are available [30]. 

The mycobacterial culture or M. tuberculosis complex acid-fast bacilli should be identified before the start of drug 
susceptibility testing. Non-tuberculous mycobacteria may have similar growth patterns but will harbour intrinsic 
resistant characteristics that will give false-resistant information. The knowledge of the exact species within the M. 
tuberculosis complex is important when interpreting the results of pyrazinamide testing, especially of M. bovis, 
which shows inherent resistance [29]. 

Laboratories should use only one reliable method for drug susceptibility testing for M. tuberculosis complex 
[13,17,28]. The laboratory should have considerable experience in the chosen method, which should be carried out 
by skilled technicians. It is also extremely important to periodically perform an internal quality control of drug 
susceptibility testing. The minimum requirement for quality control is to test each new batch of reagents. If the 
batch quality control fails, all results obtained within that batch, as well as the new batch of a reagent should be 
thoroughly reviewed and the testing should be repeated. All laboratories performing drug susceptibility testing have 
to participate additionally in an external quality control programme [13]. 

Drug susceptibility tests are usually performed on M. tuberculosis complex cultures (indirect testing), but may also 
be performed on specimens containing acid-fast bacilli known to belong to M. tuberculosis complex (direct testing) 
[7] as long as special conditions are fulfilled (see below). Results are obtained more quickly for direct testing; 
however, there is a lower success rate due to possible contamination. 

All methods described are risk level C and must be performed in a BSL3 laboratory. 

7.2 Procedure 1: General method – DST by culture 

7.2.1 Introduction 

The methods introduced in this chapter aim not only to detect resistance but also to assess susceptibility [13]. 
Applying these methods will result in high sensitivity for detecting resistance (i.e. a low rate of false susceptibility 
results) and high specificity (i.e. a low rate of false-resistance results). Additionally, these methods will also result 
in high sensitivity for assessing susceptibility (i.e. a low rate of false-resistance results) and a high specificity (i.e. a 
low rate of false susceptible results). Studies on the performance of the various methods are referenced in each 
method section.  

78 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Resistance is defined as a decrease in sensitivity of sufficient degree to be reasonably certain that the strain 
concerned is different from wild-type reference strains. In this case, the strain is unlikely to show clinical 
responsiveness to the drug. Susceptibility is defined by a level of sensitivity not significantly different from wild-type 
strains which have never come into contact with the drug. In this case, the strain is likely to show clinical 
responsiveness to the drug [8,16,22].  

Susceptibility testing methods are applied to one drug tested as a representative of a family of drugs (e.g. rifampicin 
results cover rifampicin and rifapentine, prothionamide covers ethionamide and vice-versa), or to one individual drug 
(rifampicin does not cover rifabutin and streptomycin does not cover amikacin and kanamycin). First-line drugs include 
isoniazid (H), rifampicin (R), ethambutol (E), streptomycin (S), although streptomycin is now not part of most 
standard treatments, and pyrazinamide (Z), which is usually part of the standard treatment but is not considered a 
first-line testing drug due to the difficulty in obtaining reliable results. 

Second-line drugs include the drugs used to treat MDR-TB cases, e.g. the injectables (kanamycin, capreomycin and 
amikacin), the fluoroquinolones (ofloxacin or levofloxacin, and moxifloxacin), ethionamide or prothionamide, and 
cycloserine and linezolid. Imipenem, clofazimine and clarithromycin, used sometimes for last-chance treatment of 
extensively–drug resistant TB cases (XDR-TB), i.e. MDR-TB strains with additional resistance to fluoroquinolones and 
to injectables, are not regularly tested since acquired resistance during treatment is unknown. For the new drugs, 
bedaquiline and delamanid, that became available in 2014, critical breakpoints were proposed by EUCAST/EMA but 
the methods of testing are still under investigation. In general, second-line DST is less standardised than first-line 
DST. This is due to insufficient knowledge, drug instability resulting in variation of the active concentration achieved in 
the media after preparation, and other factors.  

Due to the discrepancies in the results observed for some of the second-line drugs (cycloserine, ethionamide and 
prothionamide) or discussion about their critical concentrations, the descriptions appearing in this report will be limited 
to amikacin, capreomycin and ofloxacin [3,19,20].  

Methods are based on growth on solid media (usually egg-based, but can be synthetic), using a manual system, or in 
liquid media (usually synthetic Middlebrook media), using both automated and manual systems. Results can rely on a 
direct observation of growth, such as counting of colonies or visible liquid broth, or an indirect measure of growth 
through oxygen consumption, CO2 production or enzymatic modification of the media. 

7.2.2 Materials 

For direct testing [7]: smear-positive specimens after classic decontamination (see Section 5.6). For indirect testing 
[13,17]: cultures of M. tuberculosis complex, as a positive liquid broth or colonies on a solid media, after checking purity. 

7.2.3 Methods 

Methods mostly used in Europe include the modified proportion method on solid Löwenstein-Jensen (LJ) [9,10,14] 
and the modified proportion method in liquid Middlebrook media [2,4,5,6,26]. A less commonly used method which is 
also approved for first-line and second-line drug susceptibility testing is the resistance-ratio method [13,22]. Other 
methods which were shown to be concordant with reference methods for first-line drug susceptibility testing only are: 
the absolute concentration method and the radiometric method in liquid medium. Debated methods amongst others 
are the nitrate reductase assay and Colorimetric redox indicator (CRI) assay using resazurin; microscopically observed 
direct susceptibility testing (MODS) [1,15,18,27] and the Thin Layer Agar methods. Although these methods are 
simpler to implement than reference methods, they are less reproducible than proportion methods, probably because 
the inoculum is not monitored. 

7.2.4 Safety 

All methods described are risk level C and have to be performed in a BSL3 laboratory. Cultures or smear-positive 
specimens should be handled under a safety cabinet using sterile and disposable tips, tubes and pipettes. 

7.2.5 Report/interpretation 

Reporting of susceptibility results is easily done for each drug tested, if the method was applied correctly. Resistance 
results are preferably checked by repeated testing (clinicians should already be informed), which may in some cases 
determine the level of resistance. This may be done as soon as a resistance pattern is observed. Resistance results can 
now also be complemented by molecular detection of mutations conferring resistance, as described in Chapter 6. If a 
mutation known to confer resistance (e.g. rpo mutation leading to S531L substitution for rifampicin resistance) is 
observed, this confirms resistance. Conversely, if no mutation is observed in the genes known to confer resistance, this 
implies that the strain needs to be retested with a reference method. If the strain still appears resistant but no mutation 
is found, colonies growing in the tube containing antibiotic should be retested for molecular detection. 

Emergency and priority reporting should be carried out for cases of smear-positive pulmonary tuberculosis and for all 
cases which appear to be MDR-TB. The results should be given directly to the clinician in charge of the patient. If this is 
not possible, it should be verified that the clinician is aware of the results. Routine reporting should contain the start date 
of testing and the date of reporting. 

79 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

The level of resistance might be of interest for some first-line drugs (isoniazid, streptomycin, ethambutol) and second-line 
drugs (amikacin, capreomycin, ofloxacin, moxifloxacin) if it can be determined. Usually, a report of low resistance does 
not imply that the drug will not be given; conversely, a report of a high level of resistance implies that the drug is of no 
use to the patient. However, more clinical studies should be done correlating patient outcome with levels of resistance. 

7.3 Procedure 2: Proportion method on Löwenstein-Jensen 
medium 

7.3.1 Introduction 

The proportion method was one of the first methods described for susceptibility testing of M. tuberculosis complex. It 
was first described using the egg-based Löwenstein-Jensen (LJ) media and is considered to be a reference standard 
against which other routine methods should be assessed.  

The proportion method calculates the proportion of resistant bacilli present in a strain [12]. Below a certain 
proportion, the strain is classified as susceptible; above that proportion, it is classified as resistant. This method is well 
established for first-line and some second-line drugs. The critical proportion was assessed by a study of a cohort of 
patients in the 1960s who failed tuberculosis treatment [8,9]. Consequently, it can be used to predict clinical failure if 
the drug were to be used in monotherapy (i.e. treatment with a single drug, which would be incorrect therapy) [10]. 

7.3.2 Definition 

Resistance: The strain is presumed to be resistant when growth of more than a certain proportion of the inoculum 
occurs at a defined concentration – the critical concentration – of the drug. 

Critical concentration: The lowest drug concentration at which wild type strains do not grow. 

Critical proportion: The lowest percentage of the strain population that may grow at the critical concentration and 
which is associated with clinical ineffectiveness of that drug. 

Growth control: Culture yielded after inoculation of a tubercle bacilli suspension on a culture medium without any 
anti-TB drug in order to exhibit unrestricted growth. 

7.3.3 Materials 

A pure, well-characterised culture of M. tuberculosis bacteria in the active growth phase is necessary. Pure 
substances (no patient tablets) of the drugs must be used at all times. No special equipment is required, only tubes 
(preferably with screw caps) containing LJ medium, pipettes, and McFarland turbidity standard no. 1. 

For direct testing, smear-positive specimens are decontaminated as per the usual procedure (see Section 5.4.1.) 
and the pellet is used pure or diluted (see below). 

7.3.4 Methods 

Media preparation 
Löwenstein-Jensen tubes are used with incorporated drugs. For that, egg-based LJ is prepared according to the 
standard protocol (see standard operating procedure for preparation of LJ egg-based media) and mixed with drugs at 
the recommended quantities (Table 11) before inspissation. Screw-capped tubes containing 5 ml of the preparation 
are inspissated at 85°C for 40–45 minutes. LJ medium with and without incorporated drugs can be stored at 6+/-2°C 
for one month. 

Drugs 
The drugs to be tested should be stored according to the manufacturer’s instructions. Substances, solvents and 
dilutions are listed in Table 11 along with critical concentrations. 

Table 11. Solvents and diluents 

Solvents and diluents 

Drugs 

Isoniazid 
Rifampicin 
Ethambutol 
Streptomycin 
Capreomycin 
Amikacin 
Ofloxacin 
DW = Sterile distilled water; DMSO = dimethyl-sulfoxide; NaOH = Sodium-hydroxide. 

Substance 
Isoniazid 
Rifampicin 
Ethambutol dihydrochloride 
Dihydrostreptomycin sulfate 
Capreomycin sulfate 
Amikacin sulfate 
Ofloxacin 

Critical concentration (mg/l) 
0.2 
40 
2 
4 
40 
40 
2 

Solvents 
DW 
DMSO 
DW 
DW 
DW 
DW 
0.1N NaOH 

Diluents 
DW 
DM 
DW 
DW 
DW 
DW 
DW 

80 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Bacterial suspension and inoculation 

Indirect drug susceptibility testing 

This is carried out on a primary isolate or a subculture on LJ medium. A representative portion of the bacteria is obtained 
by sampling as many colonies as possible within one or two weeks after the appearance of growth. 

The colonies are transferred to a glass tube with physiological NaCl. The suspension can be homogenised using glass 
beads (3.0 mm in diameter) or a glass rod with a molten rounded tip by rubbing the bacteria onto the glass wall. The 
suspension should be made without residual culture medium. 

After thorough mixing and homogenisation of the suspension, the tubes should rest for 10 minutes. The supernatant 
should then be pipetted into another tube. 

The bacterial suspension used for inoculation of the culture medium should be equivalent to approximately 1 mg wet 
bacterial mass/ml (about one full loop with an inner diameter of 3 mm). 

Serial dilutions of 10–1 to 10–5 of the standard suspension are prepared by diluting sequentially 1 ml of the standard 
suspension in tubes containing 9 ml of sterile distilled 0.9% sodium chloride. 

Usually, two dilutions of the inoculum are inoculated onto the control LJ tubes (without drug): inoculum 1 and inoculum 
2, which is a 1:100 fold dilution of the inoculum 1.  

If the turbidity of the suspension is visually adjusted by comparing it to the reference suspension McFarland standard 1.0 
(9.9 ml sulphuric acid [1% volume concentration] with 0.1 ml barium chloride solution [1% mass concentration]), it will 
be equivalent to 10–2 and 10–4. Serial dilutions of 10–1 to 10–4 of the standard suspension are prepared by sequentially 
diluting 1.0 ml of the standard suspension in tubes containing 9 ml of sterile distilled 0.9% sodium chloride. 

Final dilutions of 10–2 (control 1) and 10–4 (control 2) are inoculated onto LJ as controls. The drugs containing LJ media 
are then inoculated with control 1 and control 2 inoculums. The volume of the inoculum in control and drug containing 
tubes is 0.1 ml.  

Direct testing using primary specimens 

Decontaminated smear-positive specimens are inoculated directly onto LJ slopes using two inocula: inoculum 2 is a 
1:100 dilution of inoculum 1. Dilutions are made according to the number of acid-fast bacilli per microscopic field 
(x1000 magnification): 

 
 
 

Undiluted (inoculum 1) and 10-2 (inoculum 2) if there is less than 1 AFB per field 
10-1 and 10-3 if there are 1 to 10 AFB per field 
10-2 and 10-4 if there are more than 10 AFB per field. 

Drugs containing LJ media tubes are inoculated with both inocula if possible, or at least with inoculum 1 for first-
line drugs (1% critical proportion) and inoculum 2 for second-line drugs CM, AMI, OFL (usually considered for a 
10% critical proportion). The volume of the inoculum is 0.1 ml to 0.2 ml per tube. 

There are two recommended methods of preparing the dilutions: using pipettes or a calibrated loop. Using pipettes, 
serial dilutions of 10-1 mg/ml to 10-4 mg/ml of the standard suspension are prepared by sequentially diluting 1.0 ml of 
the standard suspension (1 mg/ml) in tubes containing 9 ml of sterile distilled 0.9% sodium chloride. 

Incubation 
After inoculation, the tubes are incubated at 37°C in a slanted position, with the screw caps slightly loosened to 
allow for the evaporation of the inoculum. After 24 to 48 hours, screw caps are tightened and the tubes are further 
incubated. This does however depend on the type of screw caps; those that can be closed immediately after 
inoculation are preferable. 

7.3.5 Safety 

See general procedure in Section 7.2.4 and Chapter 1. 

7.3.6 Report interpretation 

The reading of results consists of three simple steps: 

 

 

 

Counting of colonies grown on the different slants: for dilution 1 (e.g. 10-2) a confluent growth is often 
observed since around 104 Colony Forming Units (CFU) have been inoculated; for dilution 2 (e.g. 10-4) since 
around 102 (about 20–100 colonies are counted. This number may differ from strain to strain since some are 
dysgonic and consequently the same dilution will grow less colonies; 
Calculation of the proportion of resistant bacilli by comparing counts on dilution-2 control tubes (1% of the 
dilution 1) and on drug containing tubes inoculated with the dilution 1; and 
Ratio of the calculated proportion and the critical proportion of the drug in question, in order to determine 
whether the ratio is ≥ 1 (resistant strain) or < 1 (susceptible strain). 

81 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Results are read 28 days (early reading) and 42 days (final reading) after inoculation. If after four weeks of 
incubation the proportion of resistant colonies is higher than the critical proportion, the strain can be reported as 
resistant. Moreover, if the reading on Day 28 shows that there are no colonies on the drug containing media and 
the colonies on the control tubes are mature, the strain can be reported as susceptible. With the exception of these 
two instances, all other results should be reported after the reading on Day 42. 

If the number of colonies in the control tubes inoculated with inoculum 1 is below or close to 100, the test should 
be repeated with a less diluted inoculum. 

7.4 Procedure 3: Resistance ratio method 

7.4.1 Introduction 

The resistance ratio (RR) method was one of the first methods described for drug susceptibility testing of M. 
tuberculosis complex [13,22]. It is calculated by the ratio of the minimal inhibitory concentration (MIC) of a drug 
for a patient’s strain to the MIC of the same drug for the susceptible reference strain, H37Rv, both tested in the 
same experiment. Instead of the control strain, four known sensitive strains of M. tuberculosis can be used as 
modal control MIC. Inclusion of the reference strain in each experiment not only serves as a quality-control 
measure, but also standardises results by taking into account the test variations within certain permissible limits. 
This feature makes the RR method the most accurate, but because of the use of large numbers of media units, it is 
also the most labour intensive. 

Test MIC 

Modal control MIC 

7.4.2 Materials 

= Resistance ratio 

A pure, well-characterised culture of M. tuberculosis bacteria in the active growth phase is necessary. Pure 
substances (no patient tablets) of the drugs must be used at all times. No special equipment is required, only 
plates or tubes with LJ medium and pipettes. 

7.4.3 Methods 

Calculation of modal control MIC 
Four known sensitive M. tuberculosis strains are inoculated onto a complete set (five concentrations) of drug 
containing LJ media. The plates are incubated at 37°C for two to three weeks. The modal control MIC value is 
calculated as the concentration where most of the four strains show no growth. 

Growth on the media is recorded as follows:  

 
 
 
 

CG = confluent growth; 
IC = innumerable discreet colonies; 
‘+’ = 20 to 100 colonies; 
‘-‘ = no growth or less than 20 colonies.  

The modal MIC value is calculated as follows (Table 12): 

Table 12. Calculation of modal MIC value 

Strain 

Identifier ( / ) 

Identifier ( // ) 

Identifier ( • ) 

Identifier ( •• ) 

Identifier ( ••• ) 

MIC 

A 
B 
C 
D 
Mode 

CG 
CG 
IC 
CG 
CG 

CG 
IC 
- 
IC 
IC 

Modal MIC is the 1-dot bottle. 

- 
IC 
- 
- 
- 

- 
- 
- 
- 
- 

- 
- 
- 
- 
- 

• 
•• 
// 
• 
• 

82 

 
 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Inoculation and interpretation 
Test strains are only inoculated onto the three highest antibiotic concentration egg media (1 dot, 2 dots, 3 dots) as 
the concentrations are such that the 1-dot bottle should be the modal MIC of the control strains. If the control 
strains show a higher or lower MIC than usual, this must be taken into consideration when reporting results (Table 
13). For example: 

Table 13. Examples of MIC interpretation 

Control  0.25 mg/l  0.5 mg/l  1.0 mg/l  2.0 mg/l  4 mg/l 

Ratio 

Result 

CG 
CG 
CG 
CG 
CG 
CG 
CG 
CG 
CG 

CG 

CG 

- 
- 
+ 
CG 
CG 
CG 
CG 
CG 
CG/+ 

- 
- 
- 
- 
+ 
CG 
CG 
CG 
+ 

- 
- 
- 
- 
- 
- 
+ 
CG 
+ 

MIC=1 
1/1=1 

Modal average 
Sensitive 
Sensitive 
Sensitive 
Borderline 
Resistant 
Highly resistant 
Highly resistant 
Mixed sensitive and resistant 

2/1=2 

4/1=4 

8/1=8 

Control  0.25 mg/l  0.5 mg/l  1.0 mg/l  2.0 mg/l  4 mg/l 

Ratio 

Result 

CG 
CG 
CG 
CG 
CG 
CG 
CG 
CG 

CG 

CG 

CG 
- 
+ 
CG 
CG 
CG 
CG 
CG 

- 
- 
- 
- 
+ 
CG 
CG 
CG 

- 
- 
- 
- 
- 
- 
+ 
CG 

MIC=2 
1/2=0.5 

2/2=1 

4/2=2 

8/2=4 

Modal average 
Sensitive 
Sensitive 
Sensitive 
Sensitive 
Sensitive 
Borderline 
Resistant 

Control  0.25 mg/l  0.5 mg/l  1.0 mg/l  2.0 mg/l  4 mg/l 

Ratio 

Result 

CG 
CG 
CG 
CG 
CG 
CG 
CG 
CG 

CG 

- 

- 
- 
+ 
CG 
CG 
CG 
CG 
CG 

- 
- 
- 
- 
+ 
CG 
CG 
CG 

- 
- 
- 
- 
- 
- 
+ 
CG 

MIC=0.5 
1/0.5=2 

2/0.5=4 

4/0.5=8 

8/0.5=16 

Modal average 
Sensitive 
Borderline 
Resistant 
Highly resistant 
Highly resistant 
Highly resistant 
Highly resistant 

The tests are incubated at 35–37°C for two weeks. If growth is poor at this time the tests should be re-incubated 
for another week. 

7.4.4 Safety 

See general procedure in Section 7.2.4 and Chapter 1. 

83 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

7.5 Procedure 4: Drug susceptibility testing in liquid media 
(µGIT 960) 

7.5.1 Introduction 

Egg-based medium, such as LJ, have been used for several decades. Four weeks are required to obtain results and 
the preparation of LJ tubes, although cheap, is cumbersome. Thirty years ago, the first liquid-based culture media 
were introduced commercially, and several evaluations have demonstrated good correlation with the proportion 
method and significant time savings. One of the earlier disadvantages of this system was the use of a radioactive 
labelled substrate. Because of the strict regulations of handling and waste disposal of radioactive material, it 
became necessary to develop a non-radiometric technique based on the liquid medium. 

The Becton Dickinson µGIT 960 uses 7H9 liquid media which contains an oxygen-quenched fluorochrome 
embedded in silicone at the bottom of the tube. During bacterial growth, the free oxygen is utilised and replaced 
with carbon dioxide. With the depletion of free oxygen, the fluorochrome is no longer inhibited, resulting in 
fluorescence and identification of bacterial growth, which can be detected manually or automatically [21,23-25]. 

7.5.2 Materials 

A pure, well-characterised culture of M. tuberculosis bacteria in the active growth phase is necessary. BACTEC µGIT 
tubes, along with supplements and drugs are required. Drugs are supplied as pure powder with appropriate 
solvent. 

7.5.3 Methods 

Media preparation 
A total of 0.1 ml of a reconstituted drug solution and 0.8 ml supplement (available commercially) is added to each 
of the 7 ml of 7H9 media-containing tubes.  

Drugs 
The drugs to be tested are stored according to the manufacturer’s instructions. Commercially available drugs are 
first-line drugs (isoniazid, rifampicin, ethambutol, streptomycin and pyrazinamide) and from 2015 onwards also 
second-line drugs (ofloxacin, moxifloxacin, capreomycine, amikacin, ethionamide and PAS). Critical concentrations 
are given in Table 14. 

Table 14. Critical concentrations of the most important first- and second-/third-line drugs 

Critical concentrations of the most important first-line and second/third-line drugs 

Drug 

Isoniazid 

Rifampicin 

Ethambutol  Streptomycin  Capreomycin 

Amikacin 

Ofloxacin 

Critical 
concentration 
(mg/l) 

0.1 

1 

5 

1 

2.5–3 

1–1.5 

2 

Inoculation 
The indirect drug susceptibility test can be performed from liquid or solid media, according to the manufacturer’s 
guidelines. Testing using inoculum from liquid media includes the following steps: 

 

 

 

A positive µGIT tube is used as the inoculum. The positive µGIT tube is inverted once or twice and then left 
undisturbed for about five to ten minutes to let big clumps settle to the bottom. 
The inoculum is the pure supernatant of the positive µGIT tube if positivity is observed within two or three 
days. If positivity is observed for four to five days, it has to be diluted five-fold. A volume of 0.5 ml of the 
suspension has to be added aseptically into every drug-containing tube. 
For each set of DST, the control tube will be 1:100 dilution of the original inoculum (1% control): the 
inoculum is diluted 1:100 by adding 0.1 ml of the suspension to 10 ml of sterile saline. The tube has to be 
well mixed before adding 0.5 ml into the growth-control tube. 

Incubation 
After inoculation, the tubes are incubated at 37°C in the automated BACTEC/µGIT where fluorescence is detected 
automatically. In manual operation, tubes are incubated at 37°C and are read under UV light every day. 

7.5.4 Safety 

See general procedure in Section 7.2.4 and Chapter 1. 

84 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

7.5.5 Report interpretation 

Once the growth control (i.e. 1% inoculum) is positive, after a minimum of four days (otherwise the positive signal 
is due to contamination) and a maximum of 12 days for the µGIT SIRE protocol, the instrument will compare 
growth in the drug tubes. Results are qualitative: if the drug containing tube is negative when the growth control is 
positive, the strain is reported susceptible; if the drug-containing tube is positive before or on the day the growth 
control is positive, the strain is reported resistant. If the growth control is still negative after 12 days, the test 
should be redone, checking the inoculum protocol and taking into account the time to growth of the strain 
(dysgonic). 

All positive tubes should be checked for contamination, by preparing a Gram-stained smear and/or adding one 
drop to a blood plate, and for mycobacterial growth by preparing a Ziehl-Neelsen stained smear.  

Note: A novel procedure to extend incubation for up to 30 days – where several growth controls are tested 
simultaneously to measure different proportions of resistance and several concentrations able to determine the 
level of resistance – is now proposed using the same tubes and automatically updated with the TB eXiST module. A 
protocol has been established at several European reference laboratories for tuberculosis although this still needs 
to be validated [38]. 

7.6 Procedure 5: Other methods for first-line drug 
susceptibility testing 

Many other methods or protocols have been proposed to simplify the DST procedure and circumvent the long 
duration before reporting susceptibility results for tuberculosis [1,15,18,27]. Their main advantages are relative 
simplicity, robustness and lower cost. Some are also less labour-intensive and time-consuming, which is useful when 
testing large numbers of patients in resource-limited settings. However, these methods are less reproducible, have not 
been extensively evaluated in multicentre validation studies, and are not proportion methods. For example, the 
growth is not compared to that of a 1% growth control and the inoculum is therefore not monitored so closely, 
exposing it to the risk of false resistance if the inoculum is too rich (more than 105 CFU in contact with the drug), or 
false susceptibility if the inoculum is too poor (less than 100 CFU in contact with the drug). In addition, critical 
concentrations may be different from reference methods since they were set according to the media. Selected 
methods described here are the absolute concentration method; the nitrate reductase assay; the colorimetric redox 
indicator (CRI) assay using resazurin and the microscopically observed drug susceptibility assay (MODS). 

7.6.1 Absolute concentration method 

This method is in use in Russia and some eastern European countries. The absolute concentration method is 
performed with LJ tubes containing antibiotics at the same critical concentrations as in the proportion method on 
LJ (see above). One suspension is inoculated into each tube with a control drug-free tube. After 28 days 
incubation, resistance is indicated by more than 20 colonies growing on the drug-containing LJ tube. 

7.6.2 Nitrate reductase assay 

The nitrate reductase assay (NRA) is a technique based on the capacity of M. tuberculosis to reduce nitrate to 
nitrite, which is detected by adding the Griess reagent to the medium. By incorporating 1 mg/ml potassium nitrate 
(KNO3) in the LJ medium, the reduction of nitrate can be detected using the Griess reagent, which produces a 
coloured reaction. In the presence of rifampicin or isoniazid at the critical concentration, the appearance of a red–
pink colour indicates strain growth, which is interpreted as resistance to the drug. Results can be obtained faster 
than by macroscopic detection of colonies, as the NRA uses the detection of nitrate reduction as an indicator of 
growth. 

The protocol is detailed in Angeby et al, 2002 [1] as follows: 

 

 

 
 

The LJ medium, into which 1 mg/ml potassium nitrate (KNO3) is incorporated, is prepared in 10 ml portions 
in 75- by 25-mm screw-cap glass tubes.  
Two 1 µl loops of bacteria, from fresh cultures on Löwenstein-Jensen medium, are dispensed and vortexed 
in 3 ml of phosphate-buffered saline (pH 7.4) in 7.5-ml screw-cap bottles containing a few 3-mm-diameter 
glass beads, in order to obtain the approximate turbidity of McFarland standard no. 1. 
Part of the suspension is diluted 1:10 in phosphate-buffered saline.  
For each strain, 0.2 ml of the undiluted suspension is inoculated into the tubes containing Löwenstein-
Jensen medium with KNO3 and the antibiotics and 0.2 ml of the 1:10 dilution is inoculated into three drug-
free tubes containing Löwenstein-Jensen medium with KNO3 incorporated. The three drug-free tubes serve 
as growth controls.  
 

The tubes are incubated at 37°C, and 0.5 ml of a mixture of three reagents (one part 50% (vol/vol) 
concentrated hydrochloric acid (HCl), two parts 0.2% (wt/vol) sulfanilamide, and two parts 0.1% 

85 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

(wt/vol) n-1-naphthylethylenediamine dihydrochloride, mixed shortly before use) is added to one 
drug-free control tube after seven days. 
If any colour change (strong or weak) can be seen, the corresponding antibiotic-containing tubes are 
also tested and susceptibility results are read. 
If no colour change is seen in the growth control tube, this tube is discarded and the other two 
control tubes and the antibiotic tubes are re-incubated. 
The procedure is then repeated on day 10 using the second growth control and also on day 14 using 
the last growth control tube if needed. 

 

 

 

Interpretation 
The results are classified as negative (no colour change) or ± (pale pink) to 5+ (deep red to violet). An isolate is 
considered resistant to a certain drug if there is a colour change in the antibiotic tube in question greater than that 
in the 1:10-diluted growth control on the same day. 

7.6.3 Microscopically Observed Drug Susceptibility Assay (MODS) 

The microscopically observed drug susceptibility (MODS) assay is a method for direct testing of resistance to anti-
tuberculous drugs. The sputum pellet is inoculated in microplate wells containing liquid media after 
decontamination. Cultures are examined on a daily basis using an inverted microscope [34,37]. 

Protocol 
Inoculum: one vial containing 500 ml of sample pellet is re-suspended with 2 ml of Middlebrook 7H9 broth (BD), 
oleic acid, albumin, dextrose, and catalase (OADC) (BD), and polymyxin, amphotericin B, nalidixic acid, 
trimethoprim and azlocillin (PANTA, BD), taken from one pre-prepared tube containing 5.1 ml (as per MODS 
standard operating procedure at http://ww.modsperu.org). One ml of the resuspended pellet is removed and 
stored as a backup. The remaining 1.5 ml is added to the remaining 3.1 ml of 7H9-OADC-PANTA and 900 ml of this 
final sample suspension is inoculated into each of the four wells in a 24-well tissue-culture plate (BD) as per MODS 
standard operating procedure [6]. 

For each sample, four wells are used: in two drug-free (diagnostic) wells no drug is added and each of the 
remaining two wells contain critical concentrations of either 1 mg/ml rifampicin or 0.4 mg/ml isoniazid, as per the 
MODS standard operating procedure. 

To minimise cross-contamination and occupational exposure, plates are permanently sealed inside plastic Ziploc 
bags after inoculation, and placed in an incubator (non-CO2 enriched) at 37°C. 

Wells are subsequently examined using an inverted light microscope at 400 magnification every day from day 4 
through to day 21. Positive MODS cultures are identified by presence of characteristic cord formations in the drug-
free control wells. 

Interpretation 
Growth, as observation of cord formations, in drug-free control wells but not in drug-containing wells indicates 
susceptibility. Growth observed in both the drug-free wells and the drug containing wells on the same day is 
interpreted as resistance. 

The drug concentrations to be used are as follows: isoniazid 0.4 mg/l; rifampin, 1 mg/l. 

7.6.4 Colorimetric redox indicator (CRI) assay [31,32] 

This protocol is also used for MIC determination in microplate.  

Protocol 
 

 

 
 

The inoculum is prepared from a three-week-old LJ culture re-suspended in 7H9-S medium (Middlebrook 
7H9 broth/0.1% casitone/0.5% glycerol/10% oleic acid, albumin, dextrose and catalase), adjusted to a 
turbidity equivalent to that of a 1 McFarland standard and diluted 1:10 (100 µl of the 1:10 dilution). 
The drug concentrations used are the following: rifampicin, 0.5 and 1.0 mg/l; isoniazid, 0.25 and 0.5 mg/l; 
ofloxacin, 2.0 and 4.0 mg/l; kanamycin, 2.5 and 5.0 mg/l; and capreomycin, 2.5 and 5.0 mg/l. 
A growth control containing no antibiotic and a control without inoculation are also prepared for each plate.  
The plate is covered with its lid, sealed in a plastic bag and incubated at 37°C in a normal atmosphere. 
After seven days of incubation, 30 µl of 0.02% resazurin solution is added to each well and the plate is re-
incubated for 24–48 hours. (Resazurin sodium salt is prepared at 0.02% (w/v) in distilled water, sterilised 
by filtration and stored at 48°C for no more than two weeks). 

Interpretation 
A change in colour from blue (oxidized state) to pink (reduced) indicates the growth of bacteria. When the growth 
control is positive, if wells containing drugs are positive, this indicates resistance. If wells containing drugs are 
negative, this indicates susceptibility. 

86 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

10. 

11. 

12. 

13. 

14. 

15. 

16. 

17. 

18. 

19. 

20. 

21. 

Angeby KA, Klintz L, Hoffner SE. Rapid and inexpensive drug susceptibility testing of Mycobacterium 
tuberculosis with a nitrate reductase assay. J Clin Microbiol. 2002 Feb;40(2):553-5. 

Angeby KA, Werngren J, Toro JC, Hedström G, Petrini B, Hoffner SE. Evaluation of the BacT/ALERT 3D 
system for recovery and drug susceptibility testing of Mycobacterium tuberculosis. Clin Microbiol Infect. 
2003 Nov;9(11):1148-52. 

Bai GH, Kim SJ, Chang CL; National and Regional Tuberculosis Reference Laboratories. Proficiency analysis 
of drug susceptibility testing by national-level tuberculosis reference laboratories from 1995 to 2003. J Clin 
Microbiol. 2007 Nov;45(11):3626-30. 

Bemer P, Palicova F, Rüsch-Gerdes S, Drugeon HB, Pfyffer GE. Multicenter evaluation of fully automated 
BACTEC Mycobacteria Growth Indicator Tube 960 system for susceptibility testing of Mycobacterium 
tuberculosis. J Clin Microbiol. 2002 Jan;40(1):150-4. 

Bergmann JS, Woods GL. Mycobacterial growth indicator tube for susceptibility testing of Mycobacterium 
tuberculosis to isoniazid and rifampin. Diagn Microbiol Infect Dis. 1997 Jul;28(3):153-6. 

Bergmann JS, Woods GL. Reliability of mycobacteria growth indicator tube for testing susceptibility of 
Mycobacterium tuberculosis to ethambutol and streptomycin. J Clin Microbiol. 1997 Dec;35(12):3325-7. 

Bwanga F, Hoffner S, Haile M, Joloba ml. Direct susceptibility testing for multi drug resistant tuberculosis: a 
meta-analysis. BMC Infect Dis. 2009 May 20;9:67. 

Canetti G. Present aspects of bacterial resistance in tuberculosis. Am Rev Respir Dis. 1965 Nov;92(5):687-703. 

Canetti G, Fox W, Khomenko A, Mahler HT, Menon NK, Mitchison DA, et al. Advances in techniques of 
testing mycobacterial drug sensitivity, and the use of sensitivity tests in tuberculosis control programmes. 
Bull World Health Organ. 1969;41(1):21-43. 

Canetti G, Froman S, Grosset J, Hauduroy P, Langerova M, Mahler HT, et al. Mycobacteria: laboratory 
methods for testing drug sensitivity and resistance. Bull World Health Organ. 1963;29:565-78. 

Canetti G, Rist N, Grosset J. Primary Drug Resistance in Tuberculosis. Am Rev Respir Dis. 1964 Nov;90:792-9. 

David HL. Probability distribution of drug-resistant mutants in unselected populations of Mycobacterium 
tuberculosis. Appl Microbiol. 1970 Nov;20(5):810-4. 

Drobniewski F, Rüsch-Gerdes S, Hoffner S; Subcommittee on Antimicrobial Susceptibility Testing of 
Mycobacterium tuberculosis of the European Committee for Antimicrobial Susceptibility Testing (EUCAST) of 
the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Antimicrobial susceptibility 
testing of Mycobacterium tuberculosis (EUCAST document E.DEF 8.1) – report of the Subcommittee on 
Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis of the European Committee for 
Antimicrobial Susceptibility Testing (EUCAST) of the European Society of Clinical Microbiology and Infectious 
Diseases (ESCMID). Clin Microbiol Infect. 2007 Dec;13(12):1144-56. 

Grosset J, Truffot-Pernot C, Cambau E. Bacteriology of tuberculosis. In: Reichman LB, Hershfield ES, editors. 
Tuberculosis, a comprehensive international approach. New York: Marcel Dekker; 2000. p. 157-85. 

Hausdorfer J, Sompek E, Allerberger F, Dierich MP, Rüsch-Gerdes S. E-test for susceptibility testing of 
Mycobacterium tuberculosis. Int J Tuberc Lung Dis. 1998 Sep;2(9):751-5. 

Heifets L. Drug susceptibility tests in the management of chemotherapy of tuberculosis. In: Drug 
susceptibility in the chemotherapy of mycobacterial infections. Boca Raton: CRC Press; 1991. p. 89-121 

Heifets L. Qualitative and quantitative drug-susceptibility tests in mycobacteriology. Am Rev Respir Dis. 1988 
May;137(5):1217-22. 

Hoffner S, Jimenez-Misas C, Lundin A. Improved extraction and assay of mycobacterial ATP for rapid drug 
susceptibility testing. Luminescence. 1999 Sep-Oct;14(5):255-61. 

Kim SJ. Drug-susceptibility testing in tuberculosis: methods and reliability of results. Eur Respir J. 2005 
Mar;25(3):564-9. 

Kim SJ, Espinal MA, Abe C, Bai GH, Boulahbal F, Fattorin L, et al. Is second-line anti-tuberculosis drug 
susceptibility testing reliable? Int J Tuberc Lung Dis. 2004 Sep;8(9):1157-8. 

Krüüner A, Yates MD, Drobniewski FA. Evaluation of µGIT 960-based antimicrobial testing and determination 
of critical concentrations of first- and second-line antimicrobial drugs with drug-resistant clinical strains of 
Mycobacterium tuberculosis. J Clin Microbiol. 2006 Mar;44(3):811-8. 

87 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

22.  Mitchison, DA. Sensitivity testing. In: Heaf FRG (editor). Recent advances in respiratory tuberculosis. 

London: Churchill J & A; 1968. p. 160. 

23. 

24. 

25. 

Pfyffer GE, Bonato DA, Ebrahimzadeh A, Gross W, Hotaling J, Kornblum J, et al. Multicenter laboratory 
validation of susceptibility testing of Mycobacterium tuberculosis against classical second-line and newer 
antimicrobial drugs by using the radiometric BACTEC 460 technique and the proportion method with solid 
media. J Clin Microbiol. 1999 Oct;37(10):3179-86. 

Pfyffer GE, Palicova F, Rüsch-Gerdes S. Testing of susceptibility of Mycobacterium tuberculosis to 
pyrazinamide with the non-radiometric BACTEC µGIT 960 system. J Clin Microbiol. 2002 May;40(5):1670-4. 

Rüsch-Gerdes S, Domehl C, Nardi G, Gismondo MR, Welscher HM, Pfyffer GE. Multicenter evaluation of the 
mycobacteria growth indicator tube for testing susceptibility of Mycobacterium tuberculosis to first-line 
drugs. J Clin Microbiol. 1999 Jan;37(1):45-8. 

26.  Werngren J, Klintz L, Hoffner SE. Evaluation of a novel kit for use with the BacT/ALERT 3D system for drug 

susceptibility testing of Mycobacterium tuberculosis. J Clin Microbiol. 2006 Jun;44(6):2130-2. 

27.  Wilson SM, al-Suwaidi Z, McNerney R, Porter J, Drobniewski F. Evaluation of a new rapid bacteriophage-
based method for the drug susceptibility testing of Mycobacterium tuberculosis. Nat Med. 1997 
Apr;3(4):465-8. 

28.  Woods GB, Brown-Elliott BA, Desmond EP, Hall GS, Heifets L, Pfyffer GE, et al. Susceptibility testing of 

mycobacteria, Nocardiae and other aerobic actinomycetes; approved standard, vol. 23 (18). CLSI, Wayne, PA. 

29.  Woods GL. Susceptibility testing for mycobacteria. Clin Infect Dis. 2000 Nov;31(5):1209-15. 

30.  World Health Organization. Guidelines for the programmatic management of drug-resistant tuberculosis. 

Geneva: WHO; 2008. 

31.  Martin A, Panaiotov S, Portaels F, Hoffner S, Palomino JC, Angeby K. Nitrate reductase assay for the rapid 

detection of isoniazid and rifampicin resistance in Mycobacterium tuberculosis: a systematic review and 
meta-analysis. Journal of Antimicrobial Chemotherapy (2008) 62, 56–64 

32.  Martin A, Paasch F, Docx S, Fissette K, Imperiale B, Ribon W. Multicentre laboratory validation of the 

colorimetric redox indicator (CRI) assay for the rapid detection of extensively drug-resistant (XDR) 
Mycobacterium tuberculosis. J Antimicrob Chemother 2011; 66: 827–833 

33. 

Cambau EM, Viveiros D, Machado L, Raskine C, Ritter E, Tortoli V, et al. Revisiting susceptibility testing in 
MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study. J 
Antimicrob Chemother 2014 

34.  Martin L, Coronel J, Faulx D, Valdez M, Metzler M, Crudder C, et al. A field evaluation of the Hardy TB MODS 

Kit™ for the rapid phenotypic diagnosis of tuberculosis and multi-drug resistant tuberculosis. PLoS One. 
2014 Sep 16;9(9):e107258. 

35.  Martin A, Montoro E, Lemus D et al. Multicenter evaluation of the nitrate reductase assay for drug resistance 

detection of Mycobacterium tuberculosis. J Microbiol Methods 2005; 63: 145–50. 

36.  Montoro E, Lemus D, Echemendia M, et al. Comparative evaluation of the nitrate reduction assay, the MTT 
test, and the resazurin microtiter assay for drug susceptibility testing of clinical isolates of Mycobacterium 
tuberculosis. J Antimicrob Chemother 2005; 55: 500–5. 

37.  Moore D, Evans AWC, Gilman RH, Caviedes L, Aldo Vivar JC, Sanchez E, et al. Microscopic-Observation 

Drug-Susceptibility Assay for the Diagnosis of TB. N Engl J Med. 2006 October 12; 355(15): 1539–1550. 

38. 

Springer B, et al. Quantitative drug susceptibility testing of Mycobacterium tuberculosis by use of µGIT 960 
and EpiCenter instrumentation. J Clin Microbiol, 2009. 47(6):1773-80. 

88 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

8. Molecular typing of Mycobacterium 
tuberculosis complex isolates 

Girts Skenders, Dick van Soolingen 

Revised by Stefan Niemann and Vladyslav Nikolayevskyy (2015) 

8.1 Background and principles 

In the last two decades, multiple molecular typing methods for Mycobacterium tuberculosis complex isolates have 
emerged, with different levels of reproducibility, discriminative power and demands on technical expertise. 
Previously, phage typing could only distinguish a very limited number of strain types; while today hundreds of 
thousands of different strains are recognised. At present, DNA fingerprinting supports routine contact tracing in 
many countries as well as studies on person-to-person transmission, early disease outbreak identification, high 
transmission risk groups, laboratory cross-contamination [19,20], and the distinction between reinfection and 
reactivation [3,24]. In particular, DNA fingerprinting of M. tuberculosis has greatly improved the understanding of 
TB transmission. Moreover, the recognition of genotype families has facilitated studies on the population structure 
of the M. tuberculosis complex and its transmission dynamics. 

The various DNA fingerprinting methods available serve different purposes and have variable characteristics that 
enable their use in specific applications. This chapter aims to describe the characteristics of the three most 
important and widely applied DNA fingerprinting methods: spoligotyping, MIRU-VNTR (Mycobacterial Interspersed 
Repetitive Units – Variable Number of Tandem Repeats) typing and IS6110 RFLP (Restriction Fragment Length 
Polymorphism) typing and the most important applications these typing methods can be used for. In addition, a 
perspective will be presented of using whole genome sequencing based on Next Generation Sequencing (NGS) 
technology for molecular epidemiology of the M. tuberculosis complex in the future.  

Although the application of DNA fingerprinting has improved our knowledge of the natural history of TB infections 
and the disease dynamics, there are still open questions. All DNA fingerprinting methods have different molecular 
clocks4 and the stability of DNA profiles has been studied extensively, but is not fully understood [5]. Ideally, every 
transmission results in a slight change in the DNA fingerprint, while the strains remain recognisable, which makes it 
possible to distinguish primary sources in a chain of transmission from secondary and tertiary ones, enabling much 
more detailed analysis of transmission in a given area. Unfortunately, mutations in the genome of M. tuberculosis 
complex occur according to a stochastic process and therefore DNA fingerprinting will never be a perfect tool in 
studies on transmission. However, the recent application of whole genome sequencing of M. tuberculosis isolates 
for the visualisation of transmission chains among isolates in RFLP clusters has shown that this approach may 
significantly add to the utility of the current fingerprinting methods.  

Below is an outline of the three DNA fingerprinting methods: spoligotyping, VNTR typing and RFLP typing. 

8.2 Procedure 1: Spoligotyping 

Spoligotyping is based on polymorphisms in the direct repeat (DR) locus of the mycobacterial chromosome [1,13]. 
This method utilises the amplification of variable DNA spacers in the genomic DR region of M. tuberculosis complex 
isolates as this target shows considerable strain-to-strain polymorphisms [37]. The well-conserved 36-bp direct 
repeats are interspersed with unique spacer sequences, varying from 35 to 41 bp in size. The order of the spacers 
has been found to be well conserved [38]. Currently, 94 different spacer sequences have been identified, 43 of 
which are used in the first-generation spoligotyping for M. tuberculosis complex strains [10]. After amplification, 
the denatured PCR products are applied in the reversed line on a membrane with covalently bound multiple 
synthetic spacer oligonucleotides deduced from DR region sequences of the two control strains (M. tuberculosis 
H37Rv and M. bovis BCG P3). 

Each spoligotype can then be conveniently represented as a 43-dimensional binary vector. Clinical isolates of M. 
tuberculosis complex can be differentiated by the presence or absence of one or more spacers. Almost all strains 
reveal a few (up to 43) of these spacers. Clinical specimens [21] and even paraffin-embedded samples have also 
been evaluated [33], which makes spoligotyping useful for the detection of M. tuberculosis complex in a clinical 
microbiology setting. The obtained patterns – 43 spacers present or not – are usually characteristic of a particular 
genotype family, such as the Beijing genotype strains [26]. Spoligotyping is therefore a simple, cheap, rapid and 
reproducible [15] tool to study the phylogeny of M. tuberculosis complex strains or to associate phenotypic 

4 A measure of evolutionary change over time at the molecular level that is based on the theory that specific DNA sequences 
spontaneously mutate at constant rates. This measure is chiefly used for estimating how long ago two related organisms 
diverged from a common ancestor. 

89 

 
 
 
 
                                                                    
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

features of isolates with the genotype family the bacteria represent [12]. However, with spoligotyping, the level of 
discrimination is generally low and it is necessary to be cautious when using this method to examine the TB 
transmission at strain level [16,34]. It is, however, possible to use spoligotyping as a screening method in typing 
(in the vast majority of cases strains that reveal different spoligopatterns also have different patterns when using 
other, more discriminative typing methods). On the other hand, when spoligotype patterns are identical, then no 
conclusion can be drawn regarding the epidemiological relationship between the respective patients. The SpolDB4 
database is one of the largest publicly available databases on the M. tuberculosis complex and contains spoligo 
patterns from approximately 40 000 clinical isolates representing 122 countries. 

Protocol: 

PCR: 

1.  Reconstitute dry primers Dra and DRb (Ocimum Biosolutions, India) in 2.2 ml purified water. Keep primer Dra at 

+4oC, and primer DRb at -20oC. 

2.  Prepare MasterMix for two membranes (38 test specimens plus two control DNAs) as follows: 

 
 
 
 
 
 
 

DMSO (Dimethylsulfoxide) – 50 µl 
PCR buffer (x10) – 200 µl 
µgCl2 (50 mM) – 60 µl 
dNTPs (100 mM) – 4 µl each 
Dra (reconstituted) – 100 µl 
DRb (reconstituted) – 100 µl 
Purified water – 475 µl 

3.  Set up PCRs as follows: 

 
 
 
 

MasterMix – 10 µl per tube 
Purified water – 8 µl per tube 
Taq Polymerase – 0.1 µl per tube 
Add 2 µl of crude DNA extract 

4.  Run the PCR using the following parameters: 

5 min 

94°C 

30 s 

60 s 

60 s 

94°C 

55°C 

72°C 

repeat steps 30 times 

5 min 

72°C 

End 

4°C 

∞ 

Use PCR products in hybridisation step immediately or keep for up to 72 hours at +4oC 

Hybridisation: 

The following buffers should be prepared for one membrane: 

 
 
 

2x SSPE/0.1% SDS (sodium dodecyl sulfate) – 300 ml 
2x SSPE/0.5% SDS – 1000 ml 
2x SSPE – 500 ml 

All buffers should be pre-warmed before use. 

5.  Add 20 µl of PCR products to 150 µl of2x SSPE/0.1% SDS. 
6.  Heat denature the diluted PCR products for 10 minutes at 100°C and cool on ice immediately.  
7.  Wash the membrane for five minutes at 60°C in 250 ml 2x SSPE/0.1% SDS once. 
8.  Place the membrane and the support cushion into the miniblotter, in such a way that the slots are 

perpendicular to the line pattern of the applied oligonucleotides, remove residual fluid from the slots of the 
miniblotter by aspiration. 

9.  Fill the slots with the diluted PCR products (avoid air bubbles). The first two slots should be filled with 2x 

SSPE/0.1% SDS. The two positive controls (M. tuberculosis H37Rv and M. bovis BCG DNA) should then be 
added, followed by two more slots of buffer and finally the PCR products can then be added. 

90 

 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

10.  Hybridise for 90 minutes at 60°C on a horizontal surface (no shaking). Avoid contamination of neighbouring 
slots. Before hybridisation, cover the holes at the top and bottom of the miniblotter with tape (such as 
autoclave indicator tape) to avoid evaporation. 

11.  Remove the samples from the miniblotter by aspiration and take the membrane from the mini blotter using 

forceps. 

12.  Wash the membrane twice in 250 ml 2x SSPE/0.5% SDS for 10 minutes at 60°C and allow the membrane to 

cool down to prevent inactivation of the peroxidase in the next step. 

13.  Add 5 ul streptavidin-peroxidase conjugate (500U/ml) to 20 ml of 2x SSPE/0.5% SDS. Incubate the membrane 

in this solution for 60 minutes at 42°C in a rolling bottle. Wash the membrane twice in 250 ml of 2x 
SSPE/0.5%SDS for 10 minutes at 42°C and rinse the membrane twice with 250 ml 2x SSPE for five minutes at 
room temperature. 

14.  For chemiluminescent detection of hybridising DNA, incubate the membrane for one minute in 20 ml of ECL 

detection liquid prepared by mixing equal volumes of ECL detection reagents (GE Lifesciences). 

15.  Cover the membrane with transparent plastic sheet or Saran-wrap and expose a light sensitive film (e.g. 

Amersham ECL hyperfilm available from GE Lifesciences) to the membrane for five minutes (exposure will 
depend on signal intensity and may need to be adjusted for different types of films). 

16.  Develop and fix hyperfilm, wash extensively in tap water and air dry. If the signal is too weak or too strong the 

membrane can be used again directly to expose another film for a shorter or longer period. 

17.  Binary codes could be entered into cluster analysis software (BioNumerics or similar) for further analysis. 

8.3 Procedure 2: MIRU-VNTR typing 

MIRU-VNTR typing of bacterial strains has proven to be a suitable method for the detection of genetic 
polymorphisms within bacterial species [18]. Differences in the number of tandem repeats in the 24 stretches of 
the genome of M. tuberculosis complex strains are the basis for an internationally recognised typing method which 
offers advantages over IS6110 typing. In multiplex PCRs, up to 24 loci are amplified using primers specific for the 
flanking regions of each repeat locus, after which the sizes of the amplified stretches of tandem repeats are 
determined to deduce the number of tandem repeats present. The number of tandem repeats detected at the 
different loci results in a numerical code that serves as a DNA fingerprint of the respective tuberculosis bacteria. 
This result format is another advantage over IS6110 RFLP, which allows users of this technique to exchange results 
and perform inter-laboratory comparisons. 

The determination of the PCR products in VNTR typing can be done manually by performing all single-locus PCRs, 
and then interpreting the product length using electrophoreses. It is recommended to use a molecular marker with 
multiple bands around the molecular size of interest. Using a marker containing all the different numbers of 
repeats possible for the specific locus is even better, otherwise the determination of the number of repeats is highly 
inaccurate. More automated and higher throughput methods that determine the sizes of the PCR product take 
advantage of a DNA sequencer, which labels the primers with a particular colour dye. Although this approach is 
more expensive, it saves a lot of work and is considered to be more accurate. 

Originally, VNTR typing used only 12 loci, which resulted in a limited level of discrimination [16,22,23,25]. Later on, 
more spacers were added and an international standard set of 15 and 24 loci was proposed, which made it 
possible to distinguish unrelated strains and provided the clonal stability to reliably identify isolates from the same 
transmission chain [28]. In order to have a level of discrimination comparable with RFLP typing (see below), 24 loci 
are needed, but this also makes VNTR typing labour-intensive. 

Due to the fact that VNTR typing is based on DNA amplification and hence can be performed on early positive 
cultures or even on clinical material containing sufficient bacteria, the turn-around time for this typing method is 
much shorter when compared to RFLP typing. In addition, results are presented in an easy-to-compare format and 
the method is much easier to perform than IS6110 RFLP typing, making it possible to implement VNTR typing in 
laboratories which do not have extensive molecular experience. Consequently, VNTR typing is currently considered 
to be the most suitable high-discrimination typing method. The discriminatory power of MIRU-VNTR typing for 
highly conserved genotypes, including Beijing, could be further increased by using hypervariable loci [39].  

An open database to which users can add VNTR patterns would be a powerful tool for the online analysis of the 
clonal identification of M. tuberculosis complex isolates; a first step in this direction has been taken with the launch 
of the MIRU-VNTRplus database [2]. Cluster analysis could be done locally using BioNumerics software (Applied 
Maths, Ghent, Belgium). National molecular epidemiology databases with embedded cluster analysis tools exist in 
several EU countries (e.g. United Kingdom). Cluster analysis tools are also available within international databases 
and epidemiology reporting tools, e.g. TESSY. 

Detailed protocols on multilocus MIRU-VNTR typing are available online at http://www.miru-vntrplus.org/MIRU/ 
files/MIRU-VNTRtypingmanualv6.pdf. 

91 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

8.4 Procedure 3: RFLP typing 

The restriction fragment length polymorphism (RFLP) method for typing bacterial strains has been the method most 
extensively used over the last 15 years because of its high level of discrimination [15] and reproducibility, and the fact 
that this was the first method that proved to be a suitable DNA-strain typing method for studying transmission [27]. It is 
based on the fact that the number of IS6110 insertion sequences present in the genome of strains differs from 0 to 
approximately 30. These genomic insertion sites themselves are also highly variable in M. tuberculosis complex strains, 
resulting in highly variable banding patterns.  

The generation of RFLP patterns is technically demanding and time consuming. About 2 µg of highly purified genomic 
DNA are needed as starting material. The process involves restriction enzyme cleavage of the DNA; fragment separation 
by electrophoresis; the transfer of the fragments to a DNA membrane and hybridisation by a labelled probe, and final 
visualisation of the results on a light-sensitive film. Each individual step of the process is crucial for the final result, which 
also gives an idea of the difficulties experienced with regard to inter-laboratory comparability.  

In addition, the analysis of IS6110 RFLP patterns with the BioNumerics software is complex, requiring experienced users. 
However, the difficulties associated with RFLP typing have not altered the fact that RFLP typing has revolutionised our 
understanding of TB transmission. Moreover, for strains of particular genotype families like the Beijing clade, the level of 
discrimination of RFLP typing is still superior to that of the recently introduced 24-loci VNTR typing [11,16,17]. 

8.5 General considerations on routine genotyping methods 

The three DNA fingerprinting methods described can be used for different applications. Spoligotyping is generally used 
in studies to reveal the genotype family of the respective bacteria; whereas this technique is less suitable for strain 
typing. Both RFLP and 24-loci-VNTR typing have a high level of discrimination and reproducibility and can be used for 
strain typing. As the turn-around time of VNTR typing is significantly shorter than that of RFLP typing and VNTR typing is 
also technically far less demanding, it is now considered to be the international standard in Europe and the USA. VNTR 
typing can be used in contact tracing and source-case finding and can reliably rule out transmission. Contact tracing 
complemented by genotyping is considered to be important for understanding person-to-person transmission. It is less 
clear, however, whether genotyping itself is cost-effective and has any added value beyond contact tracing from an 
immediate public health point of view [41]. 

The performance of DNA fingerprinting has also been used for predicting the size of future clusters following the 
detection of the first two cases of a new cluster. Time between the cases, age, nationality and residence are variables 
that become known shortly after the diagnosis of a new TB cluster. By combining the molecular data and the patient’s 
registration data, new cluster episodes can be predicted using the risk factors. This information can contribute to early 
warning systems for the national health services [14]. 

DNA fingerprinting can detect possible cross-contamination in the laboratory. If a laboratory detects two isolates with 
identical DNA profiles in only one week, this usually indicates a sampling or laboratory mishap [19]. In this case, the 
clinician should be asked to review the clinical picture of the patient, and the microbiologist should check the positivity 
rate of the culture and whether the cultures with identical DNA fingerprints have been contaminated at a particular stage. 
Regular checks of positive cultures are recommended to detect this common problem; in the Netherlands, about 3% of 
all positive cultures are cross-contaminated [35]. 

The widespread application of DNA fingerprinting has provided substantial insights into TB transmission, especially when 
conventional epidemiological investigation and molecular typing are combined [32]. The strong association of 
tuberculosis transmission with gender and lower age of the source case in a low-prevalence setting has been shown by 
molecular fingerprinting techniques [6]. Generally isoniazid-resistant strains have a lower potential for transmission, while 
strains with a mutation at amino acid 315 of the katG gene (one of the major mutations conferring resistance to INH) are 
as transmissible as susceptible ones [9]. Moreover, studies on transmission within and outside households in South Africa 
[29,31] has yielded important insights into the origin of TB infections in a high-prevalence setting. There is also an 
increased risk that previously treated and cured TB patients will develop TB again when reinfected [30]. 

In the European context, a study on the molecular surveillance of multidrug-resistant strains in Europe between 2003 
and 2006 showed that half of the strains genotyped by IS6110 RFLP were derived from transmission. Moreover, 84% of 
these clustered MDR-TB strains were represented by the Beijing genotype, while only 6–7% of the susceptible strains in 
Europe belong to that genotype [8]. 

8.6 Procedure 4: whole genome sequencing 

Although classic genotyping methods target highly variable genetic elements, they only interrogate a small fraction 
of the genome. Therefore, they cannot capture microevolution potentially occurring in other genomic regions. In 
contrast, NGS-based approaches give access to nearly complete genome sequences. The extended use of such 
approaches for research and epidemiological control has become possible through the rapid improvements and 
increasing affordability of NGS technologies. So-called bench top NGS systems (e.g. Illumina MiSeq) can be integrated 

92 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

into a routine workflow, with a throughput adapted to a routine microbiological laboratory [42,43]. In addition, 
commercially available easy-to-use kits for DNA library preparation and sample multiplexing now require only small 
amounts of genomic DNA, which limits the time needed to culture the slow-growing mycobacteria. 

Several studies demonstrated that, in accordance with the wider spectrum of analysis to detect genetic variation, 
whole genome-based approaches provide more resolution than classical genotyping (e.g. 24-locus MIRU-VNTR 
typing and IS6110 fingerprinting) [42,44,46-47]. In particular, whole-genome sequence analysis allows for a more 
precise differentiation of isolates belonging to a specific recent transmission chain from other, closely but not 
directly related isolates, which is especially useful in resolving complex outbreak situations [42,45,47]. In such 
situations, the phylogenetic trees based on the obtained genome-wide single nucleotide polymorphism (SNP) data 
of the isolates correlate much better with the available epidemiological data, and the spatio-temporal distribution 
patterns of the corresponding TB cases, than trees based on classic typing data [42,47]. In addition to a better 
time-dependent signal, the higher resolution offered by whole genome-based analysis also provides other valuable 
information. For example, the presence of a particularly contagious case (i.e. a super-spreader), leading to multiple 
secondary cases, can be inferred by the observation of star-like topologies in the phylogenetic tree, where clonal 
variants only differing by a few SNPs and corresponding to secondary cases branch directly from a central node, 
representing the same single source case. 

Furthermore, the identification of vacant nodes in the tree topology is suggestive of undiagnosed cases in the 
population. The unidirectional accumulation of SNPs allows a more clear-cut association of new cases with previous 
cases in a longitudinal outbreak, which may allow for more targeted contact tracing investigations [42,47]. This can 
be of use for the precise determination of the source cases for patient isolates of particular importance, such as 
MDR isolates. 

To identify and delineate recent transmission chains based on whole genome sequences, a key parameter to 
calibrate is the level of genome-wide variation that occurs in M. tuberculosis strains within and between infected 
individuals over time. In different studies, the observed levels of divergence between such longitudinal isolates 
collected from chronically-infected patients or from epidemiologically-linked cases rarely exceeded three to five 
SNPs, thus defining a cut-off range for predicting recent transmission [42,46,47]. The calculated mean rate of 
change in DNA sequence was approximately 0.5 SNPs per genome per year, providing a quantitative estimate of 
the short-term evolution rate of M. tuberculosis in the human host population [42,47]. Interestingly, this rate 
matches the mutation rate estimated for M. tuberculosis in a macaque infection model [48]. 

Compared to classic genotyping, another major advantage of whole genome sequencing is that it simultaneously 
provides direct and valuable information for predicting drug resistance, as well as highly precise phylogenetic 
identification [43]. This combination of diagnostic and epidemiological information in a single assay is a great 
benefit, especially with M. tuberculosis for which early detection of drug resistance is important. Analysis based on 
whole genome sequencing goes far beyond conventional molecular tests, focusing on known selected mutations in 
hotspot regions of genes involved in resistance to first and second-line anti-tuberculous drugs. In principle, whole 
genome sequencing captures most, if not all the gene sequences determining the so-called M. tuberculosis 
resistome, which allows interrogation of known mutations associated with drug resistance [43]. Moreover, whole 
genome sequencing at high coverage may detect the emergence and co-existence of different drug resistance-
conferring mutations before selection and fixation of a final mutant, in possible combination with compensatory 
mutations [49,50]. Such detection is of clinical relevance as the co-existence of wild-type and mutant 
subpopulations resulting in hetero-resistance may confound the current phenotypic and molecular drug resistance 
tests [49,50] as well as conclusions on transmission or secondary acquisition of drug resistance. 

Although NGS-based molecular tracing of M. tuberculosis has a vast potential, its generalised use is still hampered 
by some remaining challenges. Despite rapid cost decreases, NGS analyses still remain too costly for many 
microbiological/mycobacteriological laboratories. In addition, the bioinformatics analysis and interpretation of the 
data require adapted computer and data storage infrastructure. In contrast to classic genotyping, technical and 
analytical modalities (e.g. the precise delimitation of the genome sequence that is taken into account in the 
analysis; the minimal sequence coverage; etc.) have not yet been standardised. Consequently, datasets generated 
by different laboratories are not yet directly comparable, and universal databases are not yet available (e.g. for 
multicentric longitudinal epidemiological studies and surveillance.) For optimal prediction of drug resistance, 
although some database tools are already available such as TBDReaMDB [50], more comprehensive and well-
curated databases are needed to better and more quantitatively correlate genetic data with drug susceptibility 
phenotypes. These challenges are being addressed by large international consortia such as Patho-NGen-Trace 
(http://www.patho-ngen-trace.eu) in order to accelerate the implementation of NGS-based epidemiology and 
diagnostics. 

8.7 Materials 

Purified DNA from M. tuberculosis complex bacteria is generally the best material for molecular typing. For methods 
based on DNA amplification, such as spoligo- and VNTR typing, only a small amount is needed as starting material. 
Even purified DNA from a sufficient amount of bacteria in clinical material will result in a typing pattern. However, 
briefly incubating these bacteria in a liquid culture medium will generally yield more reliable and reproducible 

93 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

results, which is advisable because of the costs and the time to perform the typing techniques. For RFLP typing, 
based on the specific restrictions of the isolated unamplified DNA, a fully grown culture is needed as 2 µg of highly 
purified genomic DNA are required. In a diagnostic setting, it will take several weeks to achieve this amount of 
growth after TB detection. 

Membranes, reagents and positive control DNA for spoligotyping can be purchased. RFLP typing consists of a 
lengthy, multi-step laboratory procedure that is prone to error. Poor quality in RFLP typing can be connected to 
laboratory technique, but very often is caused by the incorrect interpretation of results with pattern analysis 
software. The performance of spoligotyping is better, especially in laboratories with molecular experience, and the 
results are more comparable among different laboratories [4]. 

For 24-loci VNTR typing, a kit containing all reagents for eight multiplex amplification reactions can be obtained 
commercially. In addition, the PCR product fragments are analysed on an automated DNA sequencer. In the 
absence of an expensive analyser, the 24-loci VNTR can be used with single or multiplex amplification reactions 
and detection of the product, either automated or manually (see standard operating procedure on MIRU-VNTRplus 
website at http://www.miru-vntrplus.org). The quality of international VNTR typing performance and the inter-
laboratory reproducibility has significantly improved over the last years [40]. 

8.8 Results/interpretation 

Spoligo patterns are codes of 43 possible digits and can be sorted with standard software such as Excel. However, 
most institutions use the BioNumerics software (Applied Maths, Kortrijk, Belgium), which is able to compare the 
results of any typing method. There is an international database of spoligo patterns [7] which holds tens of 
thousands of spoligo patterns that can be used to compare the locally obtained typing results with patterns that 
have been found elsewhere and are already labelled with a genotype family designation. 

The result of VNTR typing is a numerical code of usually 12, 15 or 24 numbers which can be analysed relatively 
easily, as described above in the section on spoligotyping. In epidemiological investigations local comparisons are 
best done using the BioNumerics software for which special plugins are available. There are several international 
databases with VNTR typing results in which locally obtained results can be compared with international collections 
(such as http://www.miru-vntrplus.org or http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE). 

The analysis of IS6110 RFLP patterns by BioNumerics software is technically demanding [10]. The most important 
aspect is the inclusion of internal (a mixture of two molecular markers) and external standards (DNA of a control 
strain with a suitable range of bands) for normalisation and accurate reading of the band sizes. 

8.9 Quality control 

Quality control of DNA fingerprinting is of the utmost importance. On all occasions, first-line controls should include 
strains with a known DNA fingerprint. In the case of spoligotyping, DNA of H37Rv and P3 should be included in 
each test to assess the performance of each of the 43 spacer oligonucleotide probes present on the blot. In VNTR 
typing, a strain with a known VNTR profile should be included. In RFLP typing, a particular strain with a wide range 
of bands should be used in each test to check the normalisation [4]. 

A second-line control procedure is also advised and should include the blinded exchange of a set of DNA samples 
with another laboratory twice a year to test the reproducibility. As a third-line of control, a blinded set of DNA 
samples supplied by an international organisation to multiple institutes should be analysed to test proficiency in the 
given procedure [4]. 

8.10 Biosafety 

Biosafety is a concern when carrying out DNA typing, especially when this involves heat inactivation of M. 
tuberculosis at 80°C. In some publications concern is expressed as to whether heat inactivation is sufficient to 
inactivate all bacteria. Studies have shown that even after a very long period of incubation a very limited bacterial 
growth is sometimes still observed [36]. This implies that it is advisable to perform the first steps of DNA isolation 
in a biosafety cabinet after heat inactivation at 80°C. Boiling a culture is generally considered to be a safe 
procedure to kill all bacteria. 

94 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

10. 

11. 

12. 

13. 

14. 

15. 

16. 

de Jong BC, Antonio M, Awine T, Ogungbemi K, de Jong YP, Gagneux S, et al. Use of spoligotyping and 
large sequence polymorphisms to study the population structure of the Mycobacterium tuberculosis complex 
in a cohort study of consecutive smear-positive tuberculosis cases in the Gambia. J Clin Microbiol. 2009 
Apr;47(4):994-1001. 

Allix-Béguec C, Harmsen D, Weniger T, Supply P, Niemann S. Evaluation and strategy for use of MIRU-
VNTRplus, a multifunctional database for online analysis of genotyping data an phylogentic identification of 
Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008 Aug;46(8):2692-9. 

Barnes PF, Cave MD. Molecular epidemiology of tuberculosis. N. N Engl J Med. 2003 Sep 18;349(12):1149-
56. 

Braden CR, Crawford JT, Schable BA. Quality assessment of Mycobacterium tuberculosis genotyping in a 
large laboratory network. Emerg Infect Dis. 2002 Nov;8(11):1210-5. 

de Boer AS, Borgdorff MW, de Haas PE, Nagelkerke NJ, van Embden JD, van Soolingen D. Analysis of rate of 
change of IS6110 RFLP Patterns of Mycobacterium tuberculosis based on serial patient isolates. J Infect Dis. 
1999 Oct;180(4):1238-44. 

Borgdorff MW, Nagelkerke NJ, de Haas PE, van Soolingen D. Transmission of Mycobacterium tuberculosis 
depending on the age and sex of source cases. J Epidemiol. 2001 Nov 15;154(10):934-43. 

Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, et al. Mycobacterium tuberculosis 
complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for 
classification, population genetics and epidemiology. BMC Microbiol. 2006 Mar 6;6:23. 

Devaux I, Kremer K, Heersma H, Van Soolingen D. Clusters of multidrug-resistant Mycobacterium 
tuberculosis cases, Europe. Emerg Infect Dis. 2009 Jul;15(7):1052-60. 

van Doorn HR, de Haas PE, Kremer K, Vandenbroucke-Grauls CM, Borgdorff MW, van Soolingen D. Public 
health impact of isoniazid-resistant Mycobacterium tuberculosis strains with a mutation at amino-acid position 
315 of katG: a decade of experience in The Netherlands. Clin Microbiol Infect. 2006 Aug;12(8):769-75. 

van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, et al. Strain identification of 
Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin 
Microbiol. 1993 Feb;31(2):406-9. 

Gori A, Esposti AD, Bandera A, Mezzetti M, Sola C, Marchetti G, et al. Comparison between spoligotyping 
and IS6110 restriction fragment length polymorphisms in molecular genotyping analysis of Mycobacterium 
tuberculosis. Mol Cell Probes. 2005 Aug;19(4):236-44. 

de Jong BC, Antonio M, Awine T, Ogungbemi K, de Jong YP, Gagneux S, et al. Use of spoligotyping and 
large sequence polymorphisms to study the population structure of the Mycobacterium tuberculosis complex 
in a cohort study of consecutive smear-positive tuberculosis cases in The Gambia. J Clin Microbiol. 2009 
Apr;47(4):994-1001. 

Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, et al. Simultaneous detection 
and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 
1997 Apr;35(4):907-14.  

Kik SV, Verver S, van Soolingen D, de Haas PE, Cobelens FG, Kremer K, et al. Tuberculosis outbreaks 
predicted by characteristics of First patients in a DNA fingerprint cluster. Am J Respir Crit Care Med. 2008 Jul 
1;178(1):96-104.  

Kremer K, van Soolingen D, Frothingham R, Haas WH, Hermans PW, Martín C. Comparison of methods 
based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex 
strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol. 1999 
Aug;37(8):2607-18. 

Kremer K, Arnold C, Cataldi A, Gutiérrez MC, Haas WH, Panaiotov S. Discriminatory power and 
reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin 
Microbiol. 2005 Nov;43(11):5628-38. 

17. 

Kremer K, Au BK, Yip PC, Skuce R, Supply P, Kam KM, et al. 2005. Use of variable-number tandem-repeat 
typing to differentiate Mycobacterium tuberculosis Beijing family isolates from Hong Kong and comparison 

95 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

with IS6110 restriction fragment length polymorphism typing and spoligotyping. J Clin Microbiol. 2005 
Jan;43(1):314-20. 

18. 

Lindstedt BA. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of 
pathogenic bacteria. Electrophoresis. 2005 Jun;26(13):2567-82. 

19.  Martínez M, García de Viedma D, Alonso M, Andrés S, Bouza E, Cabezas T, et al. Impact of laboratory cross-
contamination on molecular epidemiology studies of tuberculosis. J Clin Microbiol. 2006 Aug;44(8):2967-9. 

20.  Martín A, Herranz M, Lirola MM, Fernández RF; INDAL-TB group, Bouza E, et al. Optimized molecular 

resolution of cross-contamination alerts in clinical mycobacteriology laboratories. BMC Microbiol. 2008 Feb 
14;8:30. 

Qian L, Van Embden JD, Van Der Zanden AG, Weltevreden EF, Duanmu H, Douglas JT. Retrospective 
analysis of the Beijing family of Mycobacterium tuberculosis in preserved lung tissues. J Clin Microbiol. 1999 
Feb;37(2):471-4. 

Roring S, Scott AN, Glyn Hewinson R, Neill SD, Skuce RA. Evaluation of variable number tandem repeat 
(VNTR) loci in molecular typing of Mycobacterium bovis isolates from Ireland. Vet Microbiol. 2004 Jun 
10;101(1):65-73. 

Savine E, Warren RM, van der Spuy GD, Beyers N, van Helden PD, Locht C, et al. Stability of variable-
number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of 
Mycobacterium tuberculosis. J Clin Microbiol. 2002 Dec;40(12):4561-6. 

Small PM, Hopewell PC, Singh SP, Paz A, Parsonnet J, Ruston DC, et al. The epidemiology of tuberculosis in 
San Francisco. N Engl J Med. 1994 Jun 16;330(24):1703-9. 

Smittipat N, Billamas P, Palittapongarnpim M, Thong-On A, Temu MM, Thanakijcharoen P, et al. 
Polymorphism of variable-number tandem repeats at multiple loc in Mycobacterium tuberculosis. J Clin 
Microbiol. 2005 Oct;43(10):5034-43.  

van Soolingen D, Qian L, de Haas PE, Douglas JT, Traore H, Portaels F, et al. Predominance of a single 
genotype of Mycobacterium tuberculosis in countries of east Asia. J Clin Microbiol. 1995 Dec;33(12):3234-8. 

van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main 
methodologies and achievements. J Intern Med. 2001 Jan;249(1):1-26. 

Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, et al. Proposal for 
standardization of optimized mycobacterial interspersed repetitive unit - variable-number repeat typing of 
Mycobacterium tuberculosis. J Clin Microbiol. 2006 Dec;44(12):4498-510. 

Verver S, Warren RM, Munch Z, Richardson M, van der Spuy GD, Borgdorff MW, et al. Proportion of 
tuberculosis transmission that takes place in households in a high-incidence area. Lancet. 2004 Jan 
17;363(9404):212-4. 

Verver S, Warren RM, Beyers N, Richardson M, van der Spuy GD, Borgdorff MW, et al. Rate of reinfection 
tuberculosis after successful treatment is higher than rate of new tuberculosis. Am J Respir Crit Care Med. 
2005 Jun 15;171(12):1430-5. 

Verver S, Warren RM, Munch Z, Vynnycky E, van Helden PD, Richardson M, et al. Transmission of 
tuberculosis in a high incidence urban community in South Africa. Int J Epidemiol. 2004 Apr;33(2):351-7. 

de Vries G, van Hest RA, Burdo CC, van Soolingen D, Richardus JH. A Mycobacterium tuberculosis cluster 
demonstrating the use of genotyping in urban tuberculosis control. BMC Infect Dis. 2009 Sep 8;9:151. 

van der Zanden AG, Hoentjen AH, Heilmann FG, Weltevreden EF, Schouls LM, van Embden JD. Simultaneous 
detection and strain differentiation of Mycobacterium tuberculosis complex in paraffin wax embedded 
tissues and in stained microscopic preparations. Mol Pathol. 1998 Aug;51(4):209-14.  

van der Zanden AG, Kremer K, Schouls LM, Caimi K, Cataldi A, Hulleman A, et al. Improvement of 
differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by 
introduction of new spacer oligonucleotides. J Clin Microbiol. 2002 Dec;40(12):4628-39. 

Lambregts-van Weezenbeek CS, Sebek MM, van Gerven PJ, de Vries G, Verver S, Kalisvaart NA, et al. 
Tuberculosis contact investigation and DNA fingerprint surveillance in The Netherlands: 6 years’ experience 
with nation-wide cluster feedback and cluster monitoring. Int J Tuberc Lung Dis. 2003 Dec;7(12 Suppl 
3):S463-70.  

Somerville W, Thibert L, Schwartzman K, Behr MA. Extraction of Mycobacterium tuberculosis DNA: a 
question of containment. J Clin Microbiol. 2005 Jun;43(6):2996-7. 

21. 

22. 

23. 

24. 

25. 

26. 

27. 

28. 

29. 

30. 

31. 

32. 

33. 

34. 

35. 

36. 

96 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

37. 

38. 

39. 

40. 

Fang Z, Morrison N, Watt B, Doig C, Forbes KJ. IS6110 Transposition and Evolutionary Scenario of the Direct 
Repeat Locus in a Group of Closely Related Mycobacterium tuberculosis Strains. Int J Bacteriol, 1998; 
180:2102-2109. 

van Embden JDA, van Gorkom T, Kremer K, Jansen R, van der Zeijst BA, Schouls LM. Genetic variation and 
evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria J Bacteriol, 
2000;9:2393-2401. 

Allix-Béguec C, Wahl C, Hanekom M, Nikolayevskyy V, Drobniewski F, Maeda S, et al. Proposal of a 
consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat 
loci for subtyping of Mycobacterium tuberculosis Beijing isolates. J Clin Microbiol. 2014 Jan;52(1):164-72 

de Beer JL, Ködmön C, van Ingen J, Supply P, van Soolingen D; Global Network for Molecular Surveillance of 
Tuberculosis 2010. Second worldwide proficiency study on variable number of tandem repeats typing of 
Mycobacterium tuberculosis complex. Int J Tuberc Lung Dis. 2014 May;18(5):594-600  

41.  Mears J, Vynnycky E, Lord J, Borgdorff MW, Cohen T, Crisp D, et al: The prospective evaluation of the TB 

strain typing service in England: a mixed methods study. Thorax 2015. 

42.  Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al: Whole-genome sequencing to 

delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. The Lancet Infectious 
Diseases 2013, 13(2):137-146. 

43. 

44. 

45. 

a. 

46. 

47. 

Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, et al. Whole-genome sequencing for 
rapid susceptibility testing of M. tuberculosis. N Engl J Med. 2013 Jul 18;369(3):290-2 

Niemann S, Koser CU, Gagneux S, Plinke C, Homolka S, Bignell H, et al. Genomic diversity among drug 
sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PloS 
one 2009, 4(10):e7407 

Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, et al. Whole-genome sequencing and social-
network analysis of a tuberculosis outbreak. The New England Journal of Medicine 2011, 364(8):730-739. 

Schurch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, et al. High-resolution typing by integration 
of genome sequencing data in a large tuberculosis cluster. Journal of Clinical Microbiology 2010, 
48(9):3403-3406. 

Roetzer A, Diel R, Kohl TA, Ruckert C, Nubel U, Blom J, et al. Whole Genome Sequencing versus Traditional 
Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular 
Epidemiological Study. PLoS Medicine 2013, 10(2):e1001387 

Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, et al. Use of whole genome sequencing to 
estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nature Genetics 2011, 
43(5):482-486 

48. 

Sun G, Luo T, Yang C, Dong X, Li J, Zhu Y, et al. Dynamic population changes in Mycobacterium tuberculosis 
during acquisition and fixation of drug resistance in patients. J Infect Dis. 2012 Dec 1;206(11):1724-33 

49.  Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, Rüsch-Gerdes S, et al. Whole genome sequencing 

reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in 
patients. PLoS One. 2013 Dec 6;8(12):e82551 

50. 

Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB. (2009) Tuberculosis Drug 
Resistance Mutation Database. PLoS Med 6(2): e1000002. 

97 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

9. Use and validation of disinfectants for 
Mycobacterium tuberculosis 

Thomas Pottage and Allan Bennett 
Revised by Thomas Pottage and Allan Bennett (2015) 

9.1 Liquid disinfection 

There are two standard methods for the analysis of disinfectants against mycobacterial organisms including 
Mycobacterium tuberculosis (TB); they are the quantitative suspension and quantitative carrier test. These 
methods have been documented as industry standards: suspension testing EN 14348:2005 and carrier testing 
EN 14563:2008. The principle of the suspension test is to determine the efficacy of a chemical disinfectant against 
mycobacterial organisms within a suspension at a given temperature and over a set period of time. The carrier test 
is used to determine the efficacy of a disinfectant against a dried solution of Mycobacterium on a glass slide over a 
set period and at a set temperature. The strains of Mycobacterium specified in both standards are Mycobacterium 
avium (ATCC 15769) and Mycobacterium terrae (ATCC 15755), with M. terrae specified as the surrogate for M. 
tuberculosis. These micro-organisms are specified due to their lack of pathogenicity and there seems to be no 
reason why the standards could not be adapted for use with TB strains, simply by replacing the surrogate organism 
with the desired TB strain. However, replacing the strains would mean that the test would not follow the standard 
method and could not be designated as such. The standard methods, using TB surrogates, are summarised in the 
following sections. For full details the standards can be obtained from the relevant national standards body. 

This could not be stated as tested to the standard but to a method based closely on the standard, and would give more 
accurate TB disinfection results since the disinfectant would be tested on the TB strain that would be used in vitro.  

9.1.1 Suspension test: EN 14348:2005 

A test suspension of the mycobacterial agent(s) should be prepared to give a suspension concentration from 
1.5 x 109 CFU/ml to 5.0 x 109 CFU/ml. This suspension should be used on the day it is prepared. To count the stock 
suspension, dilutions of 10-7 and 10-8 should be prepared and 1 ml of the dilutions should distributed as 0.5 ml onto 
2 MCO (Middlebrook and Cohn 7H10 medium with 10% OADC enrichment) agar plates. This process should be 
performed in duplicate. The plates should then be incubated at 37 ± 1oC for 21 days. 

The disinfectant test solutions should be prepared at 1.25 times the required test concentration. This is because 
during testing, with the addition of the validation suspension (1 ml) and interfering substance (1 ml) to 8 ml of the 
disinfectant, the concentration will be diluted to 100% of the test concentration. A further two concentrations of 
the product should also be prepared for testing, with at least one of these concentrations being weaker than the 
active range concentration. The test product suspensions should be made up in hard water to the required 
concentration. 

Test products which are supplied ready-prepared for application (e.g. pre-soaked wipes) can be used but it should 
be noted in the test report that the concentration during testing will be equal to 80% and that this is the highest 
concentration achievable. Further dilutions of these ready-to-use products should be made using distilled water 
instead of hard water. 

Product test solutions should be prepared for each test and used within two hours of preparation. 

The test should be performed under two different conditions relating to the loading of organic material. This clean 
solution is prepared by adding 0.3 g of bovine albumin fraction V to 100 ml of the diluent (Tryptone sodium 
chloride solution, 1 g Tryptone, 8.5 g sodium chloride in 1000 ml water). The clean conditions will require the 
addition of 1 ml of a 3 g/l solution of Bovine albumin fraction V solution to 9 ml of the test solution and test 
product. This will give a final solution concentration of 0.3 g/l in the 10 ml test solution. 

The dirty conditions are achieved by combining a solution of bovine albumin fraction V and high concentration 
sheep erythrocytes. The solution is produced by dissolving 3 g of bovine albumin fraction V in 97 ml of diluent to 
give a solution of 30 g/l. This is diluted 1 in 10 during the test to given a final solution of 3 g/l. At least 8 ml of 
fresh defibrinated sheep blood should be centrifuged at 800 g for 10 minutes. The supernatant should be discarded 
and the erythrocytes re-suspended in the diluent. This step should be repeated at least three times until the 
supernatant has no colour. The erythrocytes can then be re-suspended and 3 ml added to 97 ml of the bovine 
albumin solution. The solution can be kept for seven days at a temperature ranging from 2°C to 8°C. 

The suspension test is performed by first pipetting 1 ml of the clean or dirty interfering solution into a sterile tube 
followed by 1 ml of the test suspension. This tube should then be placed in a water bath at the set temperature of 
20°C for two minutes. After the two minutes, 8 ml of the test product should be added to the tube and the timer 

98 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

started. The tube should be mixed at the beginning of the 60 minute test period and just before the end of the 
period. 

After the 60-minute test period, a 1 ml sample of the test solution should be removed from the tube and pipetted 
into a fresh sterile tube containing 1 ml of water and 8 ml of validated neutraliser. Pre-validation tests should have 
been conducted to ensure that the neutraliser is capable of neutralising the test product and does not inhibit the 
growth of the test organism(s). The tube should be placed in a water bath at 20°C for five minutes. 

After the neutralisation step, a 1 ml sample of the neutralised test suspension should be pipetted and distributed 
evenly between two MCO plates, in duplicate. A further 500 µl of the neutralised test suspension should then be 
taken and added to a tube containing 4.5 ml of the neutraliser. This will give a 10-1 solution of the test suspension 
which should be diluted further to 10-3 using the neutraliser. A 1 ml sample should be taken from each of the 
dilution tubes and divided between two MCO plates. This should be done in duplicate, to give four plates with 
500 µl of diluted test suspension on them. The plates should be incubated for 21 days at 37±1°C. 

The procedures for the other concentrations of the test product should be performed at the same time. 

9.1.2 Carrier Test: EN 14563:2008 

The carrier test should be performed using either M. avium (ATCC 15769) and M. terrae (ATCC 15755) or only M. 
terrae. 

A test suspension of the mycobacterial agent(s) should be prepared to give a suspension concentration from 1.5 x 
109 CFU/ml to 5.0 x 109 CFU/ml. This suspension should be used on the day it is prepared. To counting the stock 
suspension, dilutions of 10-7 and 10-8 should be prepared and 1 ml of the dilutions should distributed as 0.5 ml onto 
2 MCO (Middlebrook and Cohn 7H10 medium with 10% OADC enrichment) agar plates. This process should be 
performed in duplicate. The plates should then be incubated at 37±1°C for 21 days. 

The disinfectant test solutions should be prepared using hard water. Three preparations shall be prepared, one in 
the active concentration range and at least one below the active concentration range. 

Test products which are supplied ready-prepared for application (e.g. pre-soaked wipes) can be used directly for 
the testing. Any further dilutions of these products should use water in the place of hard water. 

The product test solutions should be prepared for each test and used within two hours of preparation. 

The disinfectant should be tested under two different conditions, with clean and dirty solutions. The procedure for 
producing these solutions is mentioned previously in the suspension test method (Suspension Test: EN 
14348:2005). 

The carrier for the test should be a glass carrier which has been frosted on one side (dimensions 15 x 60 x 1 mm). 
The carrier should be cleaned with 70% ethanol, and then a 10 mm square marked on the frosted side. Finally it 
should be sterilised in a dry heat oven. 

To inoculate the carrier 9 ml of the test suspension should be added to 1 ml of the interfering substance in a clean 
tube. The tube should be mixed and 50 µl should be pipetted into the inoculation square on the carrier and 
distributed evenly around the square using the pipette tip. The carrier should then be placed in an incubator at 
36±1°C for a maximum of 60 minutes or until it is visibly dry. The drying time should be recorded in the report 
sheet. 

The carrier test is performed by pipetting 10 ml of the test product solution into a screw cap tube (wide enough to 
accommodate the carrier slide). The tube should then be placed in a water bath at 20°C. The carriers should be 
placed into the tubes immediately after the drying process has finished, making sure the inoculation square is 
covered by the test product solution. The timer should be started immediately on immersion and the tube left for 
the 60-minute contact time. 

After the 60-minute exposure period, the carrier should be transferred to a screw cap tube filled with 10 ml of 
neutraliser and 1 ml of glass beads (diameter from 0.25 mm to 0.5 mm). Place in a water bath at 20°C then mix for 
15 seconds. The tube should then be left for a further four minutes 45 seconds, giving a total neutralisation time of 
five minutes. Pre-validation tests should have been conducted to ensure the neutraliser is capable of neutralising 
the test product and does not inhibit the growth of the test organism(s). The tube should be placed in a water bath 
at 20°C for five minutes. 

After the neutralisation period 1 ml of the neutralised solution containing the re-suspended test organisms from the 
carrier should be removed and divided equally between two MCO plates. This process should be performed in 
duplicate. Remove a further 500 µl and transfer to a tube containing 4.5 ml of neutraliser. This will give a 10-1 
solution of the test suspension which should be further diluted to 10-3 using the neutraliser. 

Take a 1 ml sample from each of the dilution tubes and divide this between two MCO plates. This should be 
performed in duplicate to give four plates with 500 µl of diluted test suspension on them. The plates should be 
incubated for 21 days at 37±1°C. 

99 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

The procedures for the other concentrations of the test product should be performed at the same time. 

9.1.3 Choice of method to be used 

The standard to be used depends on the application for which the disinfectant product is being used. For example, 
a surface disinfectant should preferably be tested using the carrier tests as that most closely matches this 
application. However, carrier tests are often thought to be more time consuming, even though there are less 
complications with the neutralisation step. The recommendation for using glass slides in the carrier test may raise 
concerns about potential for accidental abrasions in the laboratory and other materials may be considered. The 
specified 60-minute contact time will not always reflect the use of a product and it may be more realistic to reduce 
this to a shorter period, especially for the carrier test. 

9.2 Gaseous disinfection 

Gaseous decontamination has been used in microbiological laboratory facilities to decontaminate biological safety 
cabinets, equipment and the laboratory itself between experiments and before servicing [1-3]. It is often 
recommended for dealing with emergency situations such as uncontrolled releases of liquid culture in laboratories. 
Gaseous decontamination uses a vaporised chemical to contact, and in many cases condense onto, the exposed 
surfaces within the enclosure. Traditionally, gaseous lab decontamination has been undertaken using formaldehyde 
[4], where paraformaldehyde crystals are heated to sublimation or liquid formalin solution is boiled, both releasing 
formaldehyde vapour into the enclosure. This vapour then condenses onto the exposed surfaces and shows its 
disinfection properties by alkylating protein molecules when it binds to the primary amide and amino groups [2,5].  

Although it is effective as a fumigant against M. tuberculosis, even in sputum [6] and against M. bovis [7], 
formaldehyde is a potential carcinogen [4], requires a long aeration period (for removal of the vapour from the 
enclosure, unless it can be neutralised, or external ventilation is available) and the paraformaldehyde residues left 
on the surfaces can be labour intensive to remove [5,8]. These drawbacks to formaldehyde have led to 
investigations into the use of alternative gaseous decontamination technologies for fumigation.  

Of the candidates for a replacement fumigant in place of formaldehyde the best studied is perhaps hydrogen 
peroxide. The gaseous hydrogen peroxide systems were originally marketed for use in pharmaceutical clean room 
facilities, but their use has broadened to include microbiological laboratories [4], animal facilities [9], spacecraft 
assembly facilities [10] and in the hospital environment [11]. Hydrogen peroxide decontamination as a process has 
numerous advantages over formaldehyde fumigation. It leaves no residues, has better operator safety and is less 
damaging to the environment. Hydrogen peroxides works as an oxidising agent which produces hydroxyl radicals 
and superoxide anions [4] which can attack the cell’s DNA and lipids, but being highly reactive the hydroxyl radicals 
will also react with other inorganic matter and materials [2]. 

Hydrogen peroxide is marketed for fumigations in three ways: Vaporised Hydrogen Peroxide (VHP), Hydrogen 
Peroxide Vapour (HPV) and aerosolised Hydrogen Peroxide (aHP). Hydrogen peroxide plasma sterilisation, which 
introduces vaporised hydrogen peroxide in a small vacuum chamber where the contaminated equipment is placed, 
has been shown to be effective for the decontamination of contaminated instruments, such as bronchoscopes 12].  

9.2.1 Vaporised hydrogen peroxide and hydrogen peroxide vapour 

Gaseous hydrogen peroxide is produced by heating and vaporising liquid hydrogen peroxide. Liquid hydrogen 
peroxide solutions have already been shown to be an effective decontaminant against TB [13,14]. Two of the more 
established companies have different approaches for the use of the vaporised hydrogen peroxide: Steris’ 
generators use VHP and Bioquell’s HPV. 

The major differentiating factor between the two systems is the presence of microcondensation on the surfaces of 
the enclosure being fumigated. Steris’ VHP technology dehumidifies the air within the enclosure prior to injection of 
VHP. This decreases the dew point in the enclosure and allows VHP to be injected without forming condensation on 
the surfaces, meaning although VHP is injected the system is designated ‘dry’. The HPV technology designed by 
Bioquell operates in a similar fashion to formaldehyde fumigation, where HPV is injected into an enclosure above 
the dew point to allow for the formation of microcondensation on the surfaces. The microcondensate is a 
microscopic layer of hydrogen peroxide approximately 2–6 µm in thickness. Table 15 below describes more 
differences between the two technologies. 

100 

 
 
 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Table 15. Differences between the two major gaseous hydrogen peroxide technologies, Steris VHP 
and Bioquell HPV 

Parameter 

Steris 

Bioquell 

Description 
Condensation formed? 
Requires dehumidification of 
enclosure? 
Period of hydrogen peroxide 
injection 
Volume of hydrogen peroxide 
needed 
Generator located internally or 
externally in relation to enclosure 
Remote activation and monitoring 

Vaporised hydrogen peroxide 
No 

Hydrogen peroxide vapour 
Yes 

Yes 

No 

Continuous through exposure 
phase 

One injection prior to 
decontamination phase 

Large 

External 

Yes (laptop needed) 

Small 

Internal or external (dependent on 
generator chosen) 
Yes (control unit supplied extra) 

Both VHP and HPV technologies have been shown to be efficacious against a wide range of bacteria, viruses and 
prions [2,9,11,15-19], often in company sponsored trials. Gaseous hydrogen peroxide has also been shown to be 
effective at killing TB within a biological safety cabinet and high-level containment laboratories [4,20]. The 
concentration of TB used by Hall on each indicator was approximately 103 cells, this is low in comparison with the 
106 G. stearothermophilus spores on each of the other biological indicators. It was argued that the lower number 
of cells was more likely to equate to what would be remaining in a laboratory spillage after initial cleaning 
procedures were followed [20]. Kahnert’s investigation found that even if a higher concentration of TB cells were 
dried onto biological indicators (ranging from 8.0x104 to 2.3x106 CFU), no organisms were recoverable after VHP 
exposure [4]. 

9.2.2 Dry mist hydrogen peroxide 

Another way of aerosolising hydrogen peroxide within an enclosure for fumigation is to use an aerosolised 
hydrogen peroxide generator. An example of the generator, Glosair 400, is produced by Advanced Sterilisation 
Products. The aHP fumigation technique has been demonstrated to be effective against methicillin-resistant 
Staphylococcus aureus, Acinetobacter baumannii, Clostridium difficile and TB [21-24]. A comparison between aHP 
and 0.5% sodium hypochlorite solution was made by Barbut, which found the aHP more effective in killing C. 
difficile spores [22]. The aHP technology has also been successfully demonstrated against TB that had been dried 
onto stainless steel carriers (varying concentrations from 5x105 to 5x106 CFU/ml) and placed around a biosafety 
level 3 laboratory [25]. In Grare’s study 5% hydrogen peroxide was used with a 60-minute exposure period to kill 
TB, whereas a study performed by Andersen under similar conditions demonstrated that the TB was not killed after 
aHP exposure [26]. It was hypothesised that the difference in results might be due to the preparation of the TB 
indicators. In Andersen’s study, TB was dried from a saline solution whereas in Grare’s experiments TB was dried 
from a distilled water solution which might have weakened the cell membrane, making it more susceptible to aHP 
decontamination [25,26]. 

9.2.3 Plasma hydrogen peroxide 

A technology which can be employed to decontaminate smaller instruments rather than entire rooms or 
laboratories is hydrogen peroxide plasma sterilisation. The decontamination process uses a small vacuum chamber 
which is filled with vaporised hydrogen peroxide. After the vapour has diffused in the chamber, electromagnetic 
radiation is introduced to break the hydrogen peroxide molecules apart, inducing a plasma state and producing 
hydroxyl reactive species. This technology has been shown to be effective for sterilising bronchoscopes that had 
been contaminated with TB and initially decontaminated in a washer/disinfector, compared to bronchoscopes that 
had only been cleaned using a standard washer/disinfector cycle [12].  

9.2.4 Use of gaseous disinfection in accident scenarios 

Spillage of pathogenic microorganisms in a laboratory outside primary containment equipment should be an 
extremely rare event and should be prevented by employing the proper procedures and practices. The use of glass 
should be discouraged and samples should be contained when removed from primary containment using transport 
containers or bagging solutions. However there may be occasions where these precautions are impractical [25]. 

101 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

The reaction to a spill of TB in a laboratory will depend on many factors, including the sample type (diagnostic 
specimen/positive, MDR TB, titre if known, staff exposed, location, etc.) and so any recommendation is based on a 
local risk assessment. However, the following course of events will occur: 

 
 

 

An aerosol will be generated which will be gradually removed by deposition or dilution. 
There will be uncontained liquid on the laboratory floor, localised in a pool where the container lands, and 
in the form of splashes and deposited aerosols which will be widely dispersed on the laboratory floor and 
potentially on other surfaces. 
Laboratory staff exposed to the spillage should leave the location, remove contaminated garments and 
wash any exposed areas of skin immediately. The laboratory should not be entered until any aerosol has 
been removed. The time allowed should be based on information about the sample volume, titre and room 
ventilation rate. 

There are three ways that the spill can be decontaminated. 

 

 

 

Immediate gaseous disinfection, preferably using a remote system (formaldehyde or hydrogen peroxide). 
The advantage of this system is that no operator is exposed by re-entering the area. However, the 
disadvantage is that the gaseous disinfectant may not penetrate into the highest concentration material of 
the spill. This area should be subjected to a final surface disinfection stage by an experienced laboratory 
worker wearing appropriate PPE before the laboratory is re-opened. 
After a suitable period of time an experienced laboratory worker wearing appropriate PPE enters the 
laboratory and decontaminates the spill site before setting off the gaseous decontamination. The laboratory 
can then be entered directly following the gaseous disinfection. The disadvantage of this approach is the 
exposure of the worker entering the laboratory. 
Surface disinfection alone could be undertaken by a worker in PPE including RPE. The disadvantages of this 
approach are that not all contaminated surfaces may be dealt with and the worker will be exposed. 

Once again, the approach taken should be based upon a risk assessment carried out by experienced members of 
laboratory staff with biosafety expertise. It is preferable to have a risk assessment framework in place for such an 
eventuality. 

References 

Lach VH. A study of conventional formaldehyde fumigation methods. Journal of Applied Bacteriology 1990; 
68:471-477. 

Block S. Disinfection, Sterilization and Preservation. 5th ed: Lippincott Williams & Wilkins 2001. 

Luftman H, Regitis M. B. atrophaeus and G. stearothermophilus Biological Indicators for Chlorine Dioxide 
Gas Decontamination. Applied Biosafety 2008;13:143-157. 

Kahnert A, Seiler P, Stein M, et al. Decontamination with vaporized hydrogen peroxide is effective against 
Mycobacterium tuberculosis. Letters in Applied Microbiology 2005;40:448-452. 

Cheney JE, Collins CH. Formaldehyde disinfection in laboratories: limitations and hazards. British Journal of 
Biochemical Science 1995;52:195-201. 

Bensted HJ, Beveridge WIB, Downie AW, et al. eds. Disinfection of Fabrics with Gaseous Formaldehyde, 
compiled by The Committee On Formaldehyde Disinfection 1958. 

Munro K, Lanser J, Flower R. A comparative method to validate formaldehyde decontamination of biological 
safety cabinets. Applied and Environmental Microbiology 1999;65:873-876. 

Ackland NR, Hinton MR, Denmeade KR. Controlled formaldehyde fumigation system. Applied and 
Environmental Microbiology 1980;39:480-487. 

Krause J, McDonnell G, Riedesel H. Biodecontamination of animal rooms and heat-sensitive equipment with 
vaporized hydrogen peroxide. Contemporary topics 2001;40:18-21. 

Chung S, Kern R, Koukol R, Barengoltz J, Cash H. Vapor hydrogen peroxide as alternative to dry heat 
microbial reduction. Advances in Space Research 2008;42:1150-1160. 

Ray A, Perez F, Beltramini AM, et al. Use of vaporized hydrogen peroxide decontamination during an 
outbreak of multidrug-resistant Acinetobacter baumannii infection at a long-term acute care hospital. Infect 
Control Hosp Epidemiol 2010; 31: 1236-1241. 

Bar W, Marquez de Bar G, Naumann A, Rusch-Gerdes S. Contamination of bronchoscopes with 
Mycobacterium tuberculosis and successful sterilization by low-temperature hydrogen peroxide plasma 
sterilization. Am J Infect Control 2001; 29: 306-311. 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

9. 

10. 

11. 

12. 

102 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

13. 

14. 

15. 

16. 

17. 

18. 

19. 

20. 

21. 

22. 

23. 

24. 

25. 

Sattar SA, Taylor YE, Paquette M, Rubino J. In-hospital evaluation of 7.5% hydrogen peroxide as a 
disinfectant for flexible endoscopes. Can J Infect Control 1996;11:51-54. 

Dussurget O, Stewart G, Neyrolles O, et al. Role of Mycobacterium tuberculosis copper-zinc superoxide 
dismutase. Infect Immun 2001;69:529-533. 

Heckert RA, Best M, Jordan LT, et al. Efficacy of vaporized hydrogen peroxide against exotic animal viruses. 
Applied and Environmental Microbiology 1997; 63: 3916-3918. 

Rogers JV, Richter WR, Shaw MQ, Choi YW. Vapour-phase hydrogen peroxide inactivates Yersinia pestis 
dried on polymers, steel and glass surfaces. Lett Appl Microbiol 2008;47:279-285. 

Klapes NA, Vesley D. Vapour-phase hydrogen peroxide as a surface decontaminant and sterilant. Applied 
and Environmental Microbiology 1990;56:503-506. 

Kokubo M, Inoue T, Akers J. Resistance of common environmental spores of the genus Bacillus to vapor 
hydrogen peroxide. PDA J Pharm Sci Technol 1998;52:228-231. 

Fichet G, Antloga K, Comoy E, Deslys JP, McDonnell G. Prion inactivation using a new gaseous hydrogen 
peroxide sterilisation process. J Hosp Infect 2007;67:278-286. 

Hall L, Otter JA, Chewins J, Wengenack NL. Use of hydrogen peroxide vapor for deactivation of 
Mycobacterium tuberculosis in a biological safety cabinet and a room. J Clin Microbiol 2007;45:810-815. 

Piskin N, Celebi G, Kulah C, Mengeloglu Z, Yumusak M. Activity of a dry mist-generated hydrogen peroxide 
disinfection system against methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii. Am J 
Infect Control 2011. 

Barbut F, Menuet D, Verachten M, Girou E. Comparison of the efficacy of a hydrogen peroxide dry-mist 
disinfection system and sodium hypochlorite solution for eradication of Clostridium difficile spores. Infect 
Control Hosp Epidemiol 2009;30:507-514. 

Shapey S, Machin K, Levi K, Boswell TC. Activity of a dry mist hydrogen peroxide system against 
environmental Clostridium difficile contamination in elderly care wards. J Hosp Infect 2008;70:136-141. 

Bartels MD, Kristoffersen K, Slotsbjerg T, et al. Environmental meticillin-resistant Staphylococcus aureus 
(MRSA) disinfection using dry-mist-generated hydrogen peroxide. J Hosp Infect 2008;70:35-41. 

Grare M, Dailloux M, Simon L, Dimajo P, Laurain C. Efficacy of dry mist of hydrogen peroxide (DMHP) 
against Mycobacterium tuberculosis and use of DMHP for routine decontamination of biosafety level 3 
laboratories. J Clin Microbiol 2008;46:2955-2958. 

26. 

Andersen BM, Syversen G, Thoresen H, et al. Failure of dry mist of hydrogen peroxide 5% to kill 
Mycobacterium tuberculosis. J Hosp Infect 2010;76:80-83. 

103 

 
 
 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

10. Information for physicians: laboratory 
diagnosis of tuberculosis – first steps 

Dick van Soolingen, Vincent Jarlier, Francis Drobniewski 

Revised by Francis Drobniewski with contributions from Dick van Soolingen and Vincent Jarlier, 2015  

10.1 Introduction 

The diagnosis of TB is often the result of a combination of clinical, radiological, epidemiological, microbiological and 
histological data and WHO provides extensive guidance on the clinical and diagnostic management of TB [29,30]. 
Therefore, optimal communication and understanding among the different disciplines is of the utmost importance. 
The whole process of collecting clinical material for the microbiological diagnosis is delicate and each step may 
influence diagnosis. Therefore, it is vital that the collection and transportation of diagnostic material should be 
optimal. The clinical material for laboratory analysis should always be accompanied by sufficient and correct patient 
information. In the case of suspected lung TB, the patient should be provided with the appropriate sputum pots 
and detailed instructions on how to produce the most suitable sputum for TB diagnostics. Only appropriate 
approaches for obtaining, transporting and inoculating material from extra-pulmonary sites will result in the disease 
being successfully confirmed, which is also critical for surveillance and epidemiological purposes. The material 
should be kept under well-defined conditions and transported to the laboratory within defined time limits. Although 
molecular methods directly applied to clinical material are increasingly reliable in diagnosing TB and can indicate 
possible resistance to first- and second-line anti-tuberculosis drugs, the limitations associated with this approach 
(e.g. in the diagnosis of drug resistance) should be clearly indicated. The positive and negative predictive values of 
molecular tests are clearer now and reports on the presence of resistance mutations in the genome of causative M. 
tuberculosis can be accompanied by information on the weight of this finding [29,30]. 

The in vitro inhibition of growth of the causative M. tuberculosis in the presence of TB drugs in culture media 
remains the gold standard for resistance determination, but requires microbiological culture for drug susceptibility 
testing. 

M. tuberculosis is a BSL3 pathogen and each country has specific regulations on the safe transportation of these 
bacteria to referral laboratories. Communication on when and how a culture should be sent off by a peripheral 
laboratory can help to trace problems in transportation of this BSL3 pathogen. Positive M. tuberculosis cultures can 
usually, but not always, reliably confirm a TB diagnosis. This is important since sample and laboratory mislabelling, 
as well as cross-contamination, can occur. Cross-contamination rates (i.e. false-positives) of up to 3–5% of positive 
cultures have been reported. If misdiagnosis is suspected, communication between the laboratory and the 
physician involved is imperative to avoid unnecessary treatment. Often the presumptive TB diagnosis can be re-
considered by the physician in the case of false-positive cultures. Noting and discussing cross-contamination and 
other problems in the diagnosis of TB helps to improve the quality of this procedure. 

This chapter aims to increase physicians’ awareness of required quality control during the first diagnostic steps, 
particularly how these steps influence the quality of products/specimens sent to tuberculosis laboratories. It 
describes optimal sampling of clinical materials and how to obtain the best microbiological results. In addition, 
several aspects of communication between the different disciplines are described, such as the clarification and 
interpretation of laboratory results given to the clinician. It may be helpful to establish how laboratories could best 
provide clear written guidance for physicians on their requirements for optimal specimens. 

10.2 General considerations regarding the diagnosis of 
tuberculosis 

General considerations are based on WHO recommendations and guidelines [29,30] and publications listed at the 
end of the current chapter. 

Clinical material (such as sputum) for the diagnosis of TB and the initial drug susceptibility testing should be 
collected before the start of treatment.  
After collection of the sputum in a suitable container, the quality of the sputum should be directly checked 
in terms of quality and quantity. A considerable part of the sputum should be true sputum and not saliva. 
Clinical material should be collected aseptically in sterile containers of the right size and shape to avoid 
contamination with non-tuberculous mycobacteria and other microorganisms. It should be noted that tap 
water contains multiple mycobacteria of different species and therefore should not be used in this 
procedure. 

 

 

 

104 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

 

 

 

 
 

 

 

Cotton wool swabs are not suitable for use in the diagnosis of mycobacteria. Due to evaporation, the yield 
of positive cultures will drop significantly, unless the material is processed directly. Moreover, the material 
collected will generally be insufficient for TB diagnosis. 
The yield of positive results will increase for some specimens if a higher amount of the material is provided 
(in case of CSF) or multiple samples are examined. In general, and especially for dilutional fluids such as 
CSF, ascitic and pleural fluid, the largest possible volume should be collected and sent to the laboratory. 
WHO recommends examination of at least two sputa for the diagnosis of pulmonary TB. 
Short transportation times from the taking of clinical material to the laboratory can benefit diagnosis. Some 
extra-pulmonary materials may even benefit from inoculation at the bedside to increase the probability of a 
positive M. tuberculosis diagnosis. However, if inoculated at the bedside, an additional sample should be 
collected for microscopy and further diagnostic measures in case of contamination by Staphylococcus or 
other environmental organisms.  
If clinical material cannot be sent directly to the laboratory, it should be kept in a refrigerator (4°C). 
All clinical material for TB diagnosis sent to a laboratory should be accompanied by a completed form. 
Dedicated forms should be used, providing information such as the name of the patient; date of birth; 
gender; patient file number; probability of resistance to anti-tuberculosis drugs (i.e. previous history of TB, 
previous or current anti-tuberculosis treatment and country of birth); required diagnostic tests; date of 
collection; whether the sample was taken before or during treatmen, and detailed information on the 
submitting physician, including telephone number. 
If a rapid test is requested (e.g. for the detection of rifampicin resistance by molecular test), the physician 
should request this by phoning the laboratory, or using a special form and contact details should be 
provided for the rapid return of results. 
It is the responsibility of the sender to pack clinical materials appropriately. In most countries packaging is 
provided by the laboratories and generally consists of several layers of leak-proof material. The packaging 
should indicate that the material should only be opened inside an appropriate laboratory. M. tuberculosis 
cultures are a BSL3 microorganism, so special regulations apply. In principle, the biosafety regulations of 
directive 2000/54/EC [1] can be applied, but national authorities have also released individual regulations 
for the transportation of BSL3 microorganisms (see Chapter 1). It is recommended that the sender notifies 
the laboratory when the culture has been sent. Receiving laboratories should acknowledge receipt so that 
missing parcels can be traced. 

10.3 Specific considerations regarding diagnosis of 
tuberculosis 

10.3.1 Pulmonary material 

If there is a suspicion of pulmonary tuberculosis, 5–10 ml of early morning sputum should be collected in an 
appropriate sputum pot with a wide opening and a secure lid. This should be done on at least two consecutive 
days. The sputum should be freshly expectorated from the lung (rather than saliva) and the patient should be 
instructed on how to produce this material [2]. The collection of sputum over 24 hours is not recommended as the 
extended time of collection increases the chance of contamination by non-tuberculous mycobacteria and other 
bacterial microorganisms. 

If the patient is unable to produce sputum, sputum can be induced by supplying an aerosol of hypertonic saline 
solution (5% NaCl) or by collecting an early morning gastric juice sample (particularly used in young children). In 
addition, an aspirate can be obtained by bronchoscopy with a bronchial lavage. Although a routine procedure, it 
should be emphasised that carrying out a bronchoscopy in a patient suspected of TB can represent a risk to the 
person performing the procedure, and requires thorough disinfection of the bronchoscope – i.e. the procedure 
must be performed using appropriate safety standards. 

All patient material collected should be provided at the highest quality and in sufficient quantity [3]. There is not 
much known about the ex vivo survival of mycobacteria in clinical material. In one study on ZN-positive sputa kept 
at 4°C, 60% of the mycobacteria in the sputum appeared to be viable after four weeks, while at room temperature 
only 38% survived [4]. It is therefore advised to send pulmonary clinical material directly to the laboratory. If this 
is not possible, sputum samples should only be kept in the refrigerator for the minimum number of days. 

If M. tuberculosis culture is routinely performed at regional or peripheral laboratories, while additional laboratory 
procedures such as identification, drug susceptibility and typing are executed in larger laboratories and/or NRLs, it 
is of the utmost importance that positive cultures are sent to the centralised facility without delay. 

In difficult field conditions, the use of a transport medium may be considered and this includes the use of 1% 
cetyl-pyridinium chloride in 2% sodium hydroxide. This solution can be mixed in equal quantities with patient 
material and it results in mycobacteria which remain viable for at least eight days. However, the disadvantage of 
this approach is that the bacteria subsequently only grow on Löwenstein-Jensen medium and not on 7H10 or other 
agar-based media [5]. Other alternatives have been developed and are undergoing evaluation. 

105 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

10.3.2 Pleural material 

If pleural fluid is obtained, the chance of a positive culture can be improved by having increased volumes, which 
can then be concentrated. The largest volume possible should be taken and sent. However, recent studies have 
shown that the transport medium, place of inoculation and type of inoculation medium influence the yield of 
mycobacteria. Bedside inoculation in combination with a liquid Mycobacterium spp. medium appear to be the best 
choice. Alternatively, containers with heparin should be used to avoid clotting and trapping of mycobacteria [6]. 
Pleural fluid aspiration and pleural biopsy may increase diagnostic yield. 

10.3.3 Lymphadenitis material 

For the diagnosis of tuberculous lymphadenitis, lymph node biopsy (ideal) and fine-needle aspiration are the first-
choice diagnostic methods in both low-incidence and endemic countries [6, 7, 8]. In the case of a negative fine 
needle aspiration, an excision biopsy should be considered, which often results in a higher chance of positive 
microscopy for mycobacteria. A fine-needle aspirate should be taken using a 19- or 21-gauge needle; the sample 
needs to be transported directly to the microbiological/pathological laboratory to prevent evaporation. It is 
important to inform both the pathologist and the microbiologist beforehand that the delicate clinical material is to 
be dealt with immediately.  

Under no circumstances should the material for microbiological examination be placed in formalin (used for the 
histopathological specimen) as it will kill any TB bacteria present.  

10.3.4 Gastric juice 

Investigation of gastric fluid is recommended in the diagnosis of pulmonary TB when examination of sputum or 
bronchial lavage fluid is not possible, for example in young children. Fasting gastric fluid should be collected after 
the administration of 20–30 ml of physiological saline in 5–10 ml of sodium carbonate (Na2CO3). The material 
should be transported to the laboratory within four hours. The investigation of gastric fluid can also be useful in the 
case of immunocompromised patients who are unable to provide sputum [9]. 

10.3.5 Peritoneal fluid 

If tuberculous peritonitis is suspected, at least 5–10 ml ascitic fluid can be collected and sent, or inoculated at the 
bedside in a liquid mycobacteria culture medium. However, in a review involving more than a thousand patients, a 
peritoneal biopsy appeared more sensitive [10,11]. In general, sending the largest possible volume for 
centrifugation at the laboratory is ideal. 

10.4 Information flow from microbiologist to physician and 
instructions regarding tuberculosis diagnosis 

Physicians should provide basic patient information and specimen(s) to the laboratory that needs this information 
to guide its work, interpret the results and participate in TB surveys at local, regional, national and international 
levels. The information should include at a minimum gender and date of birth, postal code, country of birth and 
ideally history of anti-tuberculous treatment and HIV status where possible. When laboratory results are reported 
to the physician, a basic level of information should always be provided to avoid mistakes and confusion, including 
date of specimen reception at the laboratory, test date, patient identifiers, results and a clear interpretation of the 
results. Physicians should demand an unambiguous clarification of the results if required. In the case of 
microscopic examination, (semi-)quantitative results of the number of bacteria/field (WHO) scales are helpful. If a 
peripheral or regional laboratory has already performed diagnostic tests, it is very helpful if these results are sent 
together with the culture to a centralised laboratory to avoid duplication or allow confirmation. 

For cultures, the quantitative results in terms of time to positivity (in days) for liquid medium are helpful 
(particularly where the samples have been sent to indicate treatment progress) and possibly the number of 
colonies on solid medium could be stated. A low number of colonies on a primary culture, unusual timings for 
positive cultures (e.g. a higher than usual positivity rate associated with inoculation on or around the same day, or 
a very short time to positivity in a smear-negative extra-pulmonary sample) may raise serious suspicions of cross 
contamination and the laboratory needs to be aware of this. If suspected, positive cultures found on consecutive 
days can be subjected to VNTR typing (DNA fingerprinting, see Chapter 8). If they reveal the same profile, cross-
contamination is highly likely. 

In addition, the results of nucleic-acid amplification tests (NAATs) should be provided using appropriate wording 
and context; overall validity depends on the use of inhibition/amplification controls, negative and positive controls, 
and the positive and negative predictive value. For example, when an NAAT is positive while the microscopic smear 
is negative, it should be explained that the positive predictive value of this result is highly dependent on the 
prevalence of tuberculosis in the respective patient category. 

106 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

There has been substantial progress in the development of new diagnostic tests for both TB and drug resistance 
12,13]. However, not all mutations are associated with clinically-relevant resistance. This should always be clearly 
stated. Large-scale studies that confirmed molecular test results by phenotypic drug resistance testing showed 
close concordance for rifampicin resistance (as a surrogate for MDR-TB) [14] and clearly demonstrated the value of 
such testing systems, provided appropriate controls are used. Therefore, these tests can be used to direct the 
therapy and the choice of anti-tuberculosis drugs. However, the true resistance profile of the causative bacteria 
should be measured with an in vitro growth inhibition method, although this requires much more time than 
molecular tests. For instance, the detection of rifampicin susceptibility with a molecular test (if no rpo mutations 
are found) indicates with more than 95% certainty that the strain is indeed susceptible to rifampicin. The molecular 
tests for the detection of isoniazid (INH) resistance are less precise. If no mutations are found in the katG gene or 
in the inhA promotor, there is still a 10–25% chance that the respective bacteria are resistant to INH. 

Nevertheless, with modern, automated (e.g. GeneXpert) and semi-automated/manual (line probe assays), the 
presence of mutations associated with rifampicin or isoniazid resistance are generally predictive of phenotypic 
resistance, although the predictive value varies [15-21]. Multiple trials in the second half of the twentieth century 
clearly demonstrated the high probability of treatment failure with laboratory-defined MDR first-line drugs. 
Clinicians can therefore respond to these laboratory results by amending patient therapy and instituting appropriate 
infection control measures. 

Molecular assays to detect aminoglycoside and fluroquinolone resistance have been developed and are accurate for 
rapidly identifying resistance in M. tuberculosis cultures and heavily smear-positive sputum specimens [22-25]. 
Novel lab and/or POC tests for the diagnosis of TB, rifampicin, isoniazid, fluoroquinolone, and aminoglycoside 
resistance (XDR) are under development and showing promise, with several currently undergoing large-scale 
evaluation studies.  

Small population studies have compared the use of whole genomic sequencing of TB strains as either adjunct tests 
or as potential replacement for current phenotypic/genotypic systems. Moreover, whole genome sequencing 
approaches for DST have been combined with molecular epidemiology analysis to examine transmission in 
outbreaks [26-28]. 

Finally, clinicians should understand the limitations of all these testing systems: for rifampicin and isoniazid 
laboratory-defined resistance is predictive of clinical failure; for other drugs the test might give fairly reliable results 
(e.g. prothionamide) but not necessarily be clinically predictive and for some drugs it is arguable whether there are 
any reliable tests (e.g. cycloserine). This emphasises the need for support when taking clinical decisions related to 
the choice of drugs for treatment. 

References 

1. 

2. 

3. 

4. 

5. 

6. 

7. 

8. 

Directive 2000/54/EC of the European Parliament and of the Council of 18 September 2000 on the 
protection of workers from risks related to exposure to biological agents at work (seventh individual 
directive within the meaning of Article 16(1) of Directive 89/391/EEC). Available from: https://eur-
lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A32000L0054. 
Enarson D, Rieder H, Arnadottir T, Trébucq A. Technical guide: sputum examination for tuberculosis by 
direct microscopy in low income countries. Fifth edition. Paris: International Union Against Tuberculosis and 
Lung Disease; 2000. Available from: http://www.uphs.upenn.edu/bugdrug/antibiotic_manual/IUATLD_afb 
microscopy_guide.pdf. 
Peterson EM, Nakasone A, Platon-DeLeon JM, Jang Y, de La Maza LM, Desmond E. Comparison of direct and 
concentrated acid-fast smears to identify specimens culture positive for Mycobacterium spp. J Clin Microbiol. 
1999 Nov;37(11):3564-8. 
Banda HT, Harries AD, Boeree MJ, Nyirenda TE, Banerjee A, Salaniponi FM. Viability of stored sputum 
specimens for smear microscopy and culture. Int J Tuberc Lung Dis. 2000 Mar;4(3):272-4. 

Smithwick RW, Stratigos CB, David HL. Use of cetylpyridinium chloride and sodium chloride for the 
decontamination of sputum specimens that are transported to the laboratory for the isolation of 
Mycobacterium tuberculosis. J Clin Microbiol. 1975 May;1(5):411-3. 

Cheng AF, Tai VH, Li MS, Chan CH, Wong CF, Yew WW, et al. Improved recovery rate of Mycobacterium 
tuberculosis from pleural aspirates: bedside inoculation, heparinized containers and liquid culture media. 
Scand J Infect Dis. 1999;31:485-7. 
Bekedam HJ, Boeree M, Kamenya A, Liomba G, Ngwira B, Subramanyam VR, et al. Tuberculous 
lymphadenitis, a diagnostic problem in areas of high prevalence of HIV and tuberculosis. Trans R Soc Trop 
Med Hyg. 1997 May-Jun;91(3):294-7. 

Prasoon D. Acid-fast bacilli in fine needle aspiration smears from tuberculous lymph nodes. Where to look 
for them. Acta Cytol. 2000 May-Jun;44(3):297-300. 

107 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

9. 

10. 

11. 

12. 

13. 

14. 

15. 

16. 

John GT, Juneja R, Mukundan U, Date A, Vincent L, Jacob CK, et al. Gastric aspiration for diagnosis of 
pulmonary tuberculosis in adult renal allograft recipients. Transplantation. 1996 Mar 27;61(6):972-3. 
Chow KM, Chow VC, Szeto CC. Indication for peritoneal biopsy in tuberculous peritonitis. Am J Surg. 2003 
Jun;185(6):567-73. 
Muneef MA, Memish Z, Mahmoud SA, Sadoon SA, Bannatyne R, Khan Y. Tuberculosis in the belly: a review of forty-
six cases involving the gastrointestinal tract and peritoneum. Scand J Gastroenterol. 2001 May;36(5):528-32. 

Drobniewski F, Nikolayevskyy V, Maxeiner H, Balabanova Y, Casali N, Kontsevaya I. Rapid diagnostics of 
tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to 
implementation. BMC Med. 2013 Aug 29;11:190. 
Drobniewski F, Nikolayevskyy V, Balabanova Y, Bang D, Papaventsis D. Diagnosis of tuberculosis and drug 
resistance: what can new tools bring us? Int J Tuberc Lung Dis. 2012 Jul;16(7):860-70. 

Sam IC, Drobniewski F, More P, Kemp M, Brown T. Mycobacterium tuberculosis and rifampin resistance, United 
Kingdom. Emerg Infect Dis. 2006 May;12(5):752-9. 
Hillemann D, Rüsch-Gerdes S, Richter E. Evaluation of the GenoType MTBDRplus assay for rifampin and isoniazid 
susceptibility testing of Mycobacterium tuberculosis strains and clinical specimens. J Clin Microbiol. 2007 
Aug;45(8):2635-40. 

Brossier F, Veziris N, Truffot-Pernot C, Jarlier V, Sougakoff W. Performance of the genotype MTBDR line probe 
assay for detection of resistance to rifampin and isoniazid in strains of Mycobacterium tuberculosis with low- and 
high-level resistance. J Clin Microbiol. 2006 Oct;44(10):3659-64. 

17.  Mironova S, Pimkina E, Kontsevaya I, Nikolayevskyy V, Balabanova Y, Skenders G, et al. Performance of the 

GenoType® MTBDRPlus assay in routine settings: a multicenter study. Eur J Clin Microbiol Infect Dis. 2012 Jul;31 
(7):1381-7. 
Seoudi N, Mitchell SL, Brown TJ, Dashti F, Amin AK, Drobniewski FA. Rapid molecular detection of tuberculosis 
and rifampicin drug resistance: retrospective analysis of a national UK molecular service over the last decade. 
Thorax. 2012 Apr;67(4):361-7. 

Bowles EC, Freyée B, van Ingen J, Mulder B, Boeree MJ, van Soolingen D. Xpert MTB/RIF®, a novel automated 
polymerase chain reaction-based tool for the diagnosis of tuberculosis. Int J Tuberc Lung Dis. 2011 Jul;15(7):988-9. 
Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S, Krapp F, et al. Rapid Molecular Detection of Tuberculosis 
and Rifampin Resistance. N Engl J Med. 2010 Sep 9;363(11):1005-15. 
Steingart KR, Schiller I, Horne DJ, Pai M, Boehme CC, Dendukuri N. Xpert® MTB/RIF assay for pulmonary 
tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev. 2014 Jan 21;1:CD009593. 

Hillemann D, Rüsch-Gerdes S, Richter E. Feasibility of the GenoType MTBDRsl assay for fluoroquinolone, 
amikacin-capreomycin, and ethambutol resistance testing of Mycobacterium tuberculosis strains and clinical 
specimens. J Clin Microbiol. 2009 Jun;47(6):1767-72. 
Kontsevaya I, Ignatyeva O, Nikolayevskyy V, Balabanova Y, Kovalyov A, Kritsky A, et al. Diagnostic Accuracy of the 
GenoType MTBDRsl Assay for Rapid Diagnosis of Extensively Drug-Resistant Tuberculosis in HIV-Coinfected 
Patients. J Clin Microbiol. 2013, 51:243-8. 

Ignatyeva O, Kontsevaya I, Kovalyov A, Balabanova Y, Nikolayevskyy V, Toit K, et al. Detection of Resistance to 
Second-Line Antituberculosis Drugs by Use of the Genotype MTBDRsl Assay: a Multicenter Evaluation and 
Feasibility Study. J Clin Microbiol. 2012 May;50(5):1593-7. 
Theron G, Peter J, Richardson M, Barnard M, Donegan S, Warren R, et al. The diagnostic accuracy of the 
GenoType(®) MTBDRsl assay for the detection of resistance to second-line anti-tuberculosis drugs. Cochrane 
Database Syst Rev. 2014 Oct 29;10:CD010705. 
Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, et al. Genomic analysis identifies targets of 
convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013 Oct;45(10):1183-9. 

Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, et al. Evolution and transmission 
of drug-resistant tuberculosis in a Russian population. Nat Genet. 2014 Mar;46(3):279-86. 
Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, et al. PolyTB: A genomic variation 
map for Mycobacterium tuberculosis. Tuberculosis (Edinb). 2014 May;94(3):346-54. 

18. 

19. 

20. 

21. 

22. 

23. 

24. 

25. 

26. 

27. 

28. 

29.  World Health Organization. Implementing tuberculosis diagnostics. Policy framework. Geneva: WHO; 2015. 

Available from: http://www.who.int/tb/publications/implementing_TB_diagnostics. 

30.  World Health Organization. Treatment of tuberculosis: guidelines. Fourth edition. Geneva: WHO, 2009. Available 

from: http://www.who.int/tb/publications/2010/9789241547833. 

108 

 
 
 
TECHNICAL REPORT 

Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

Annex 1. Network partners 

This list, which was revised by Yen Holicka in 2015, includes both former and current contributors to the project. 

Name of participant 

Alexander Indra 

Vanessa Mathys 
Predecessor: Maryse Fauville-Dufaux 

Elizabeta Bachiiska 

Despo Pieridou-Bagatzouni 

Vera Katalinic-Jankovic 

Ilona Zemanová 
Predecessor: Marta Havelkova 
Troels Lillebæk 
Predecessor: Vibeke Østergaard Thomsen 
Tiina Kummik 

Hanna Soini  
Maternity cover: Merja Marjamaki 
Vincent Jarlier 

Emmanuelle Cambau 

Sabine Rüsch-Gerdes  

Dimitrios Papaventsis  

Nóra Szabó 

Aniko Guba  

Gudrun Sigmundsdottir 
Predecessor: Ingibjörg Hilmarsdóttir 
Margaret Fitzgibbons 
Predecessor: Noel Gibbons  

Lanfranco Fattorini 

Daniela Cirillo 
Girts Skenders 

Sabine Erne  
Edita Pimkina 

Paul Reichert 
Julie Haider 
Predecessor: Karl Galea 
Dick van Soolingen 

Institution/country 

AGES – Institute for Medical Microbiology and Hygiene, 
Department for Mycobacteriology and Clinical Molecular 
Biology, Vienna, Austria 
Institute Scientifique de Santé Publique (WIV-ISP) 
Reference Laboratory Tuberculosis and Mycobacteria, 
Scientific Institute of Public Health, Brussels, Belgium 
National Reference Laboratory of TB, National Centre of 
Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria 
Microbiology Department (MPHS), Nicosia General Hospital, 
Nicosia, Cyprus 
Croatian National Mycobacterium Reference Laboratory, 
Croatian National Institute of Public Health (CNIPH), 
Zagreb, Croatia 
National Reference Laboratory for Mycobacteria, Prague, 
Czech Republic 
International Reference Laboratory of Mycobacteriology, 
Statens Serum Institut (SSI), Copenhagen, Denmark  
Department of Mycobacteriology, United Lab, Tartu 
University Hospital (TUH), Tartu, Estonia  
Mycobacterial Reference Laboratory, National Institute for 
Health and Welfare (THL), Turku, Finland 
Bacteriology-Hygiene, Pitié-Salpêtrière hospital, Paris, 
France  
Laboratoire de Microbiologie, Hopital Saint Louis, Paris, 
France 
National Reference Laboratory for Mycobacteria, 
Forschungszentrum Borstel, Borstel, Germany 
National Reference Laboratory for Mycobacteria (NRLM), 
Sotiria Chest Diseases Hospital, Athens, Greece 
National Mycobacterium Reference Laboratory, Budapest, 
Hungary 
Northern Hungarian Regional Institute of National Public 
Health and Medical Officers' Service, TB Laboratory, Miskolc, 
Hungary 
Department of Microbiology, Landspitali University Hospital, 
Reykjavik, Iceland 
Irish Mycobacteria Reference Laboratory (IMRL), 
Microbiology Department, Central Pathology Laboratory, St. 
James's Hospital, Dublin, Ireland  
Dipartimento di Malattie Infettive, Parassitarie e 
Immunomediate, Istituto Superiore di Sanità (ISS), Rome, 
Italy  
Fondazione Centro San Raffaele (FCSR), Milan, Italy  
Mycobacteriology Department of Laboratory, State Agency 
‘Latvian Infectology Center’, Upeslejas, Latvia  
Amtsärztin, Office for Public Health, Vaduz, Liechtenstein 
National TB Reference Laboratory, National Tuberculosis 
and Infectious Diseases University Hospital (VULSK), Vilnius, 
Lithuania 
Laboratoire National de Santé (LNS), Luxembourg 
Mater Dei Hospital, Malta 

National Institute for Public Health and the Environment 
(RIVM), Bilthoven, Netherlands 

109 

 
 
 
Handbook on tuberculosis laboratory diagnostic methods in the European Union – Updated 2018 

TECHNICAL REPORT 

Name of participant 

Institution/country 

Anne Torun Mengshoel 
Predecessor: Turid Mannsåker 

Ewa Augustynowicz-Kopec 
Predecessor: Zofia Zwolska 

Anabela Santos Silva 
Predecessor: Anabela Medo Miranda 

Maria Joao Simoes 
Predecessor: Susana David 

Ionela Mutean 
Daniela Homorodean 

Monika Polanova 
Predecessor: Juraj Trenkler 

Manca Zolnir 

Maria Soledad Jimenez Pajares 

Sofia Samper  

Sven Hoffner 

Huma Simsek 
Predecessor: Ismail Ceyhan and Nurhan Albayrak 

Francis Drobniewski 

Yen Holicka 
Predecessor: Sarah Mitchell 

Vladyslav Nikolayevskyy 

Emma Huitric 
Marieke van der Werf 
Predecessor: Davide Manissero 
Andreas Sandgren 
Csaba Ködmön 
Predecessors: Alexandra Clarici and Amanda Ozin 

National Reference Laboratory for Mycobacteria, Norwegian 
Institute of Public Health (NIPH), Division of Infectious 
Disease Control, Department of Bacteriology and 
Immunology, Oslo, Norway 
Microbiology Department in National Tuberculosis and Lung 
Diseases Research Institute. National Reference TB 
Laboratory, Warsaw, Poland 
National Mycobacterium Reference Laboratory (NMRL), 
National Institute of Health ‘Dr. Ricardo Jorge’, Porto, 
Portugal 
Instituto Nacional de Saúde ‘Dr. Ricardo Jorge’, 
Departamento de Doenças Infecciosas, Laboratório Nacional 
de Referência das Infecções, Respiratórias para 
Micobactérias, Lisbon, Portugal  
Pneumophtisiology Hospital, Brasov, Romania 
Spitalul Clinic de Pneumologie ‘Leon Daniello’ (PNEUMO), 
Laboratorul National de Referinta pentru Micobacterium, 
Cluj- Napoca, Romania 
National Institute for Tuberculosis, Lung diseases and 
Thorax Surgery, National Register for Tuberculosis, Vysne 
Hagy, Slovakia 
National Reference Laboratory for Mycobacteria, University 
Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia 
Laboratorio de Micobacterias, Servicio de Bacteriología, 
Centro Nacional de Microbiología. Instituto de Salud Carlos 
III, Madrid, Spain 
Laboratorio de Investigación Molecular (I+CS), Hospital 
Universitario Miguel Servet, Edificio de Consultas Externas, 
Zaragoza, Spain 
National Reference Laboratory for Tuberculosis, The Public 
Health Agency of Sweden, Solna, Sweden 
National Tuberculosis Reference Laboratory, Communicable 
Diseases Research Department, Refik Saydam National 
Public Health Agency, Ankara, Turkey 
Public Health England (PHE, previously Health Protection 
Agency-HPA), National Mycobacterium Reference 
Laboratory, Clinical TB and HIV Group, Centre for Infectious 
Diseases, Barts and the London School of Medicine, London, 
UK  
Public Health England (PHE, previously Health Protection 
Agency-HPA), National Mycobacterium Reference Laboratory, 
Clinical TB and HIV Group, Centre for Infectious Diseases, 
Barts and the London School of Medicine, London, UK  
Public Health England (PHE, previously Health Protection 
Agency-HPA), National Mycobacterium Reference Laboratory, 
Clinical TB and HIV Group, Centre for Infectious Diseases, 
Barts and the London School of Medicine, London, UK  
ECDC, Tuberculosis Programme, Stockholm, Sweden 
ECDC, Tuberculosis Programme, Stockholm, Sweden 

ECDC, Tuberculosis Programme, Stockholm, Sweden 
ECDC, Tuberculosis Programme, Stockholm, Sweden 

110 

 
 
 
 
European Centre for Disease 
Prevention and Control (ECDC)

Address:	 
Gustav	III:s	boulevard	40,	SE-169	73	Solna,	
Sweden

Tel.	+46	858601000
Fax	+46	858601001
www.ecdc.europa.eu 

An agency of the European Union
www.europa.eu

Subscribe to our publications 
www.ecdc.europa.eu/en/publications

Contact us 
publications@ecdc.europa.eu

 Follow us on Twitter 

@ECDC_EU

 Like our Facebook page 
www.facebook.com/ECDC.EU

ECDC is committed to ensuring the transparency and independence of its work

In accordance with the Staff Regulations for Officials and Conditions of Employment of Other Servants of the European Union and the 
ECDC  Independence  Policy,  ECDC  staff  members  shall  not,  in  the  performance  of  their  duties,  deal  with  a  matter  in  which,  directly  or 
indirectly,  they  have  any  personal  interest  such  as  to  impair  their  independence.  Declarations  of  interest  must  be  received  from  any 
prospective contractor(s) before any contract can be awarded.
www.ecdc.europa.eu/en/aboutus/transparency

HOW TO OBTAIN EU PUBLICATIONS

Free publications:

•	 one	copy: 

via	EU	Bookshop	(http://bookshop.europa.eu);

•	 more	than	one	copy	or	posters/maps: 

from	the	European	Union’s	representations	(http://ec.europa.eu/represent_en.htm);	 
from	the	delegations	in	non-EU	countries	(http://eeas.europa.eu/delegations/index_en.htm);	 
by	contacting	the	Europe	Direct	service	(http://europa.eu/europedirect/index_en.htm)	or 
calling 00 800 6 7 8 9 10 11 (freephone number from anywhere in the EU) (*).

(*)	The	information	given	is	free,	as	are	most	calls	(though	some	operators,	phone	boxes	or	hotels	may	charge	you).

Priced publications:

•	 via	EU	Bookshop	(http://bookshop.europa.eu).