Extensively drug-resistant tuberculosis (TB) continues to challenge care and control in the WHO European Region, despite generally low incidence across the European Union and European Economic Area (EU/EEA). Treatment outcomes remain poor for the most resistant forms of disease, increasing the importance of timely diagnosis and accurate drug resistance detection. Within a region characterised by high laboratory capacity, population mobility and heterogeneous epidemiology, consistent diagnostic strategies are essential.
An EU/EEA diagnostic algorithm has been proposed to align practice with WHO recommendations while reflecting regional realities. The approach integrates rapid molecular testing, systematic culture and routine use of whole genome sequencing (WGS), with phenotypic drug susceptibility testing (pDST) applied selectively to support efficient, high-value diagnostics.
Rationale for a Region-Specific Diagnostic Approach
The EU/EEA brings together low TB incidence with concentrated risk in specific populations, including migrants from high-burden countries, older adults and immunosuppressed individuals. In 2023, 38,993 TB cases were reported across the region, corresponding to 8.6 cases per 100,000 population. Despite this relatively low burden, a substantial proportion of cases involve rifampicin-resistant or multidrug-resistant TB (RR/MDR-TB), particularly in certain countries and risk groups. Free movement across borders further amplifies the need for early detection and comparable diagnostic standards.
Low incidence can reduce routine clinical exposure and weaken incentives to maintain complex diagnostic pathways. At the same time, resistance patterns and cross-border transmission demand rapid and comprehensive resistance profiling. WHO algorithms emphasise universal access to molecular rapid diagnostic tests followed by additional testing to detect broader resistance. Their effectiveness in the EU/EEA depends on adaptation to local epidemiology, laboratory capacity, referral networks and testing volumes. In low-incidence settings, test sequencing must also account for pre-test probability and positive predictive value to avoid unnecessary testing while preserving diagnostic accuracy.
Access to drug susceptibility testing across the EU/EEA is described as stable but uneven. In 2023, 80% of bacteriologically confirmed pulmonary TB cases were tested for rifampicin resistance, and more than 70% had first-line drug susceptibility results. Among RR/MDR-TB cases, 60% were tested for fluoroquinolone resistance, and nearly all pre-extensively drug-resistant cases had results for at least one additional Group A drug. Variation between countries, combined with persistently poor outcomes in extensively drug-resistant TB, supports the case for a more harmonised regional algorithm.
Current Diagnostic Practices in EU/EEA Laboratories
A survey conducted in August 2024 by the European Reference Laboratory Network for Tuberculosis assessed diagnostic algorithms used in 23 EU/EEA countries. Most laboratories reported using molecular WHO-recommended rapid diagnostic tests alongside smear microscopy as primary diagnostics. Line probe assays were used as initial tests for first-line resistance detection in 14 countries, while moderate-complexity nucleic acid amplification tests were reported by 17 countries.
Culture was universally performed to confirm TB diagnosis. Phenotypic susceptibility testing for first-line drugs was routine in almost all countries, with two laboratories limiting first-line pDST to isolates with resistance-associated mutations identified through WGS. Second-line pDST was generally reserved for selected cases. Genotypic susceptibility testing was largely centralised, with 13 countries using WGS systematically and two applying targeted next-generation sequencing. Participation in external quality assessment for sequencing-based genotyping increased markedly, from 13 laboratories in 2017 to 20 in 2024.
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These findings indicate substantial molecular capacity but also variability in implementation. Many laboratories operate both culture and sequencing workflows, creating potential for duplication and inefficiency without clear guidance on test sequencing. The increasing recognition of non-tuberculous mycobacteria, reported in several EU/EEA countries, adds complexity, as these infections can resemble TB clinically. Culture remains essential for differentiating these pathogens and supports broader diagnostic yield.
Key Features of the Proposed EU/EEA Algorithm
The proposed algorithm places molecular rapid diagnostic tests at the front of the pathway for universal detection of Mycobacterium tuberculosis complex and initial screening for rifampicin resistance, with optional testing for isoniazid and fluoroquinolones depending on local epidemiology. A defining element is the systematic use of culture regardless of molecular results or resistance status. This ensures isolated availability for further testing, supports detection of non-tuberculous mycobacteria and underpins downstream phenotypic and genotypic analyses.
Smear microscopy is positioned primarily as an indicator of infectiousness to inform isolation measures. It also supports evaluation of suspected non-tuberculous mycobacterial infection when molecular tests for TB are negative and is used to monitor treatment response over time.
Following culture positivity, routine WGS is proposed to generate comprehensive genotypic drug susceptibility profiles. These data inform treatment adjustments for both drug-susceptible and drug-resistant TB, with particular emphasis on RR/MDR-TB and isoniazid-resistant disease. In the EU/EEA context, WGS also enables detection of cross-border transmission clusters and supports surveillance, contact tracing and coordinated public health responses.
Phenotypic susceptibility testing remains integral but is applied strategically. Its main roles include confirmation of resistance profiles, investigation of mutations with uncertain clinical significance and support for treatment decisions involving new or repurposed drugs. Under the algorithm, pDST is focused on isolates with resistance-associated mutations in key drug groups or mutations not yet fully characterised. Genotypically susceptible first-line results are not routinely confirmed phenotypically, concentrating laboratory resources where genotypic sensitivity is limited.
Targeted next-generation sequencing is described as an additional option when culture or WGS is unavailable, delayed or constrained by limited bioinformatics capacity. It may support rapid regimen initiation or adjustment in RR/MDR-TB and isoniazid-resistant TB, although phenotypic testing remains necessary due to lower sensitivity for some drugs. Targeted sequencing is also highlighted in situations with increased risk of bedaquiline resistance.
The proposed EU/EEA TB diagnostic algorithm reflects a deliberate shift towards sequencing-led diagnostics in a low-incidence but high-capacity setting. By combining universal rapid molecular testing with systematic culture and routine WGS, while reserving phenotypic testing for defined scenarios, the approach aims to improve efficiency without compromising accuracy. Beyond individual patient care, the routine use of WGS strengthens surveillance and cross-border coordination in a mobile region. Sustained investment in laboratory capacity, harmonisation of practices and data sharing remain central to addressing drug-resistant TB and improving outcomes across the EU/EEA.
Source: The Lancet Regional Health – Europe
Image Credit: iStock
