Tuberculosis molecular surveillance status report, focusing on rifampicin and multi-drug resistance in the EU/EEA
The European Centre for Disease Prevention and Control (ECDC) has analysed whole genome sequencing (WGS) profiles of rifampicin resistant (RR)- and multi-drug resistant (MDR) Mycobacterium tuberculosis strains, collected between 2020 and 2023 in the European Union (EU) and European Economic Area (EEA). The results were added to tuberculosis (TB) WGS data collected during the period 2017−2019 as a part of an EU/EEA pilot project on TB molecular surveillance.
Analysis of 2 726 RR/MDR TB isolates with complete WGS data showed:
- a sub-optimal typing coverage at EU/EEA level. Only 11 countries contributed, with 751 strain sequences during the period 2020−2023;
- wide variation in the sequencing coverage. The highest sequencing coverage was achieved in 2018 (69.0%), while the lowest coverage was observed in 2023 (17.1%);
- a decreasing clustering proportion from 2020. The lowest clustering percentage was observed in 2023 (21.2%) and the highest in 2020 (62.0%);
- the identification of 68 cross-border molecular clusters, comprising 650 RR/MDR TB strains in total. Only 18 clusters included 10 or more strains, involving two to ten countries in each cluster;
- limitations due to the incompleteness of data for some non-mandatory variables (e.g. country of birth/nationality). As a consequence, in-depth analyses of cluster dynamics and possible transmission routes within the clusters was not possible;
- successful lineage assignment in 97.3% of the strains. The most prevalent lineages were Beijing (N=1 033, 37.9%), Mainly T (N=561, 20.6%) and Haarlem (N=320, 11.7%). Due to the low number of countries submitting WGS data during the period 2020−2023, Beijing lineage appeared to be a dominant strain, however this should be interpreted with caution.
The COVID-19 pandemic had a significant impact on TB laboratory services in the EU/EEA, and the engagement of the EU/EEA countries remains low, 10 countries in 2023 compared to 23 countries in 2018 and 2019.
In conclusion, despite the support and IT infrastructure available at ECDC, efforts are still needed to consolidate the WGS-based surveillance of TB in the EU/EEA in order to achieve the 2017−2019 level as a minimum (i.e. typing coverage above 50%). A higher WGS typing coverage will contribute to a better understanding of rifampicin RR/MDR TB strain diversity, early detection and tracing of trans-national outbreaks and the mapping of transmission routes across Europe, as well as changes in the resistance pattern and mechanism.
