Guidance

Appendix 2: Investigations for TB Disease (Active TB)

Published 6 October 2026

The key diagnostic investigations for TB disease referred to in this guidance are summarised below. These investigations inform risk assessment of the relative infectiousness of a case of TB.

Chest X-ray (CXR)

Chest X-ray is usually the first screening and diagnostic tool for pulmonary TB, being accessible, low-cost, and valuable for identifying the presence and severity of pulmonary TB. CXR is almost always abnormal in individuals who have a competent immune system and active pulmonary TB. TB typically presents as fibronodular opacities in the upper lobes with or without cavities on a CXR. The presence of cavities on CXR is associated with infectiousness.

Computerised Tomography (CT)

If a CXR does not produce a clear enough image or is not definitive, a computerised tomography (CT) scan may be undertaken. This is effectively a series of X-rays taken from different angles to form detailed images. A CT scan can detect more subtle signs that might indicate TB than CXR.

Positron emission tomography (PET)-CT, and magnetic resonance imaging (MRI) are other imaging modalities which may be used, depending on the location of disease within the body.

Sputum Acid-Alcohol Fast Bacilli (AAFB) Smear/ Acid Fast Bacilli (AFB)

The bacteria that cause TB, Mycobacterium tuberculosis, settle and multiply deep in the lungs. When a person with TB coughs, mucus from the lungs (sputum) contains these bacteria. The sputum that is produced is used to test for TB bacteria using microscopy which is known as a ‘smear test’ where the bacteria can be stained and seen under a microscope. Acid‑Alcohol Fast Bacilli (AAFB or AFB) are bacteria that retain a special stain even after being treated with acid‑alcohol. Mycobacterium tuberculosis, the bacterium that causes TB, is an acid‑fast bacillus because of its thick, waxy cell wall. In AAFB testing, sputum is tested for the presence of M. tuberculosis bacteria.

Sputum may be spontaneously coughed up (expectorated) by the patient or induced (with appropriate precautions to prevent transmission). Induced sputum is a procedure used for patients who have trouble producing sputum spontaneously, where nebulised hypertonic saline is used to liquify airway secretions, promote coughing and allow expectorations for capture and microbiological testing. Three consecutive samples should be collected where possible (minimum 8 hours apart, including an early morning specimen), although one good quality sample is often sufficient for diagnosis.

The sputum is examined in the laboratory using a fluorescent stain (now first-line over acid-fast staining, as this is more sensitive), then confirmed with Ziehl-Neelsen (ZN)-staining to confirm presence bacilli consistent with M. tuberculosis. Other organisms, especially non-tuberculous mycobacteria, may also stain positive. Refer to the UKHSA UK Standards for Microbiology Investigations here for more information.

If the sputum is positive for bacilli, the results will be graded to indicate the number of bacteria present. This may range from 1+ to 3+ or 4+ depending on number of organisms seen and the grading system. Smear positivity and its grading may help estimate the degree of infectiousness and burden of TB, with the caveat that results may be dependent on the quality of the specimen and experience of the operator. TB culture, with subsequent WGS via the reference laboratory should then be performed.

The WHO target is that by 2027 everyone should have a M. tuberculosis polymerase chain reaction (PCR) as a first diagnostic test (85).

Bronchoalveolar lavage

Bronchoalveolar lavage (BAL) is a procedure performed during a bronchoscopy to collect a sample from the lungs for testing. During the procedure, a saline solution is put through the bronchoscope to wash the airways and capture a fluid sample. BAL can be used to obtain respiratory specimens from patients with suspected pulmonary TB who are sputum-scarce or sputum smear-negative (patients who are smear-negative may still be culture positive).

Sputum culture

Culture is the most sensitive and specific test for pulmonary TB. It should always be performed where possible as it is required for precise identification and for drug sensitivity testing and genetic typing. A positive culture proves the presence of live Mycobacterium tuberculosis and confirms active TB disease, not latent infection. It is more sensitive than smear microscopy, especially when bacterial numbers are low. Growth on solid media may take up to 8 weeks; growth in liquid media may be detected in 1 to 3 weeks (86).

Mycobacterial (non-TB and TB) PCR

Molecular amplification techniques such as PCR are more sensitive and specific than smear microscopy. They also approach the sensitivity of culture and are faster, and may provide early information regarding drug-resistance (87). Molecular detection of mycobacteria may be especially useful where there is a high clinical suspicion and a rapid diagnosis of TB would have a positive impact on patient management or infection control (for example confirmation of smear positive sample before contact tracing, or where there is a high probability of infection with MDR-TB).

Molecular testing cannot replace mycobacterial culture for more complete drug sensitivity testing and WGS, and culture should still be done on all samples.

Whole genome sequencing (WGS)

Once mycobacteria have grown and been isolated in culture, the DNA is extracted for WGS processing. In approximately 90% of cases, the WGS result provides speciation (the type of mycobacteria, for example M. tuberculosis or nontuberculous mycobacteria) (70). If the species is M. tuberculosis, WGS provides antibiotic susceptibility and determines how closely related an isolated strain is to other isolated strains within the laboratory collection (67).

Susceptibility testing is conducted for all people with culture-confirmed TB. Confirmed cases are subcategorised by susceptibility of the TB strain causing their infection to the different antibiotic agents commonly used in treatment as per the following WHO definitions (88):

• fully sensitive TB: TB caused by M.tuberculosis sensitive to all first line agents
• rifampicin-resistant TB (RR-TB): TB caused by M.tuberculosis resistant to rifampicin with or without resistance to other first-line anti-TB drugs
• multidrug resistant TB (MDR-TB): TB caused by M.tuberculosis resistant to at least isoniazid and rifampicin
• pre-extensively drug resistant (pre-XDR) TB: TB caused by M. tuberculosis that is resistant to rifampicin and is also resistant to any fluoroquinolone (levofloxacin or moxifloxacin).
• extensively drug resistant TB (XDR-TB): TB caused by M. tuberculosis that is resistant to both rifampicin and any fluoroquinolone, and is resistant at least one additional ‘Group A’ drug (bedaquiline or linezolid) (89)

References

See the attached list of references for TB contact tracing guidance.