TECHNICAL DOCUMENT Handbook on TB laboratory diagnostic methods in the European Union www.ecdc.europa.eu ECDC TECHNICAL DOCUMENT Handbook on TB laboratory diagnostic methods for the European Union 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 which was included as an annex. This report has now been revised, updated and renamed as the ‘Handbook on TB laboratory diagnostic methods for the European Union’. Suggested citation: European Centre for Disease Prevention and Control. Handbook on TB laboratory diagnostic methods for the European Union, Stockholm: ECDC; 2016. Stockholm, March 2016 ISBN 978-92-9193-739-4 doi 10.2900/216384 Catalogue number TQ-01-16-109-EN-N © European Centre for Disease Prevention and Control, 2016 Reproduction is authorised, provided the source is acknowledged ii Handbook on TB laboratory diagnostic methods for the EU TECHNICAL DOCUMENT Contents Abbreviations ................................................................................................................................................ v Background and introduction .......................................................................................................................... 1 1 Biosafety in the laboratory diagnosis of tuberculosis ....................................................................................... 4 1.1 Background and principles ................................................................................................................... 4 1.2 The containment laboratory (biosafety level 3) ...................................................................................... 5 1.3 The laboratory facility .......................................................................................................................... 6 1.4 Procedures ......................................................................................................................................... 7 1.5 Personal protective equipment (PPE)..................................................................................................... 7 1.6 The human resource component .......................................................................................................... 8 1.7 Specific laboratory tasks related to hazards ........................................................................................... 8 2 Quality assurance ...................................................................................................................................... 12 2.1 Background and principles ................................................................................................................. 12 2.2 Selection and implementation of tests ................................................................................................. 13 2.3 Validation ......................................................................................................................................... 13 2.4 Control and trend monitoring by key indicators .................................................................................... 14 2.5 Physical and environmental conditions ................................................................................................ 14 2.6 Equipment ........................................................................................................................................ 14 2.7 Management and staff ....................................................................................................................... 14 2.8 Documentation and registration .......................................................................................................... 15 2.9 Sampling guidance, review of requests and service to customers ........................................................... 15 2.10 Subcontracting, services and supplies ................................................................................................ 15 2.11 Complaints, errors and corrective actions ........................................................................................... 15 2.12 Improvements................................................................................................................................. 15 2.13 Reporting and releasing results ......................................................................................................... 16 3. Diagnosis of latent TB infection ................................................................................................................. 17 3.1 Background and principles ................................................................................................................. 17 3.2 The tuberculin skin test (TST) ............................................................................................................ 18 3.3 Interferon-γ release assays (IGRAs) .................................................................................................... 18 4. Smear microscopy .................................................................................................................................... 32 4.1 Background and principles ................................................................................................................. 32 4.2 Procedure 1: Ziehl-Neelsen (ZN) ......................................................................................................... 32 4.3 Procedure 2: Fluorochrome staining .................................................................................................... 34 4.4 Sample collection .............................................................................................................................. 35 4.5 Smear preparation ............................................................................................................................ 36 4.6 Staining procedures ........................................................................................................................... 36 4.7 Microscopy ....................................................................................................................................... 37 4.8 Recording and reporting .................................................................................................................... 38 4.9 Quality control .................................................................................................................................. 40 5. Culture tests for Mycobacterium tuberculosis complex ................................................................................. 42 5.1 Background and principles ................................................................................................................. 42 5.2 Biohazards and biosafety in the TB laboratory ...................................................................................... 42 5.3 Specimen collection, storage and transport .......................................................................................... 44 5.4 Homogenisation and decontamination of specimens ............................................................................. 45 5.5 Culture media: principles ................................................................................................................... 49 5.6 Solid media ....................................................................................................................................... 49 5.7 Culture tube inoculation ..................................................................................................................... 50 5.8 Culture incubation ............................................................................................................................. 51 5.9 Culture examination .......................................................................................................................... 51 6. Identification of M. tuberculosis and drug resistance in cultures/sputum using molecular assays and immunoassays .. 54 6.1 Background and principles ................................................................................................................. 54 6.2 Procedure 1: Chromatographic immunoassay for the qualitative detection of Mycobacterium tuberculosis complex from cultures ........................................................................................................................................... 54 6.3 Procedure 2: Line probe assay for identification of the genus Mycobacterium and 16 different mycobacterial species including M. tuberculosis complex from culture .............................................................................. 55 6.4 Procedure 3: Line probe assay for identification of M. tuberculosis complex and detection of rifampicin resistance in M. tuberculosis ............................................................................................................................................. 57 6.5 Procedure 4: Line probe assay for identifying species from genus Mycobacterium