External quality assessment for identification, antimicrobial susceptibility testing and molecular typing of Streptococcus pneumoniae, 2026

Invasive pneumococcal disease remains a major public health issue in Europe, particularly among young children and older adults. Surveillance requires reliable identification of Streptococcus pneumoniae (S. pneumoniae) , serotype determination, AST and, increasingly, genomic characterisation. Serotype information is particularly important for monitoring vaccine-preventable disease, serotype replacement and the distribution of non-vaccine serotypes.

This EQA was organised within the IBDLabNet framework on behalf of ECDC to assess current EU/EEA laboratory capacity for the detection and characterisation of S. pneumoniae in both non-culture and culture-based settings. The exercise included a shared non-culture panel and an optional pneumococcal culture panel. Samples were shipped in December 2025, the online response form opened in January 2026, and the submission deadline was 15 April 2026.

A total of 34 EU/EEA laboratories from 24 countries were included in the EU/EEA analysis. All 34 EU/EEA laboratories received the non-culture panel, and 32/34 submitted at least one non-culture sample result in REDCap. The pneumococcal culture panel was requested by 24 EU/EEA laboratories, with 23 EU/EEA laboratories providing analysable isolate-level results.

Overall, performance was strong for culture-based species identification. Correct identification was reported by 23/23 laboratories (100.0%) for both P1 and P2 samples. Culture-based serotyping was also high: 19/23 laboratories (82.6%) correctly reported P1 sample as serotype 23F, and 21/23 (91.3%) correctly reported P2 sample as serotype 14. When restricted to laboratories reporting an interpretable serotype result, concordance was 19/21 (90.5%) for P1 and 21/21 (100.0%) for P2 samples. AST uptake was high, with MIC testing reported by 21/23 laboratories (91.3%) for P1 and 20/23 (87.0%) for P2. WGS was reported by 11/23 laboratories (47.8%) for each isolate; among WGS-positive submissions, sequence type was reported for 22/22 (100.0%) and LINcode for 16/22 (72.7%).

Non-culture species detection was also high for both pneumococcal non-culture samples. Correct pathogen identification was 28/31 (90.3%) for NC3, expected to contain serotype 14, and 28/31 (90.3%) for NC5, expected to contain serotype 23F. Serotype reporting from non-culture material was less complete. Correct serotype assignment among all laboratories with an interpretable pathogen response was 7/31 (22.6%) for NC3 and 6/31 (19.4%) for NC5. However, among laboratories reporting an interpretable serotype result, concordance was high: 7/8 (87.5%) for NC3 and 6/7 (85.7%) for NC5. These findings indicate that the main limitation was incomplete progression from pneumococcal detection to usable serotype information, rather than frequent incorrect serotype assignment among laboratories providing interpretable serotype results.

The EQA confirms strong isolate-based pneumococcal identification and generally high culture-based serotyping performance among participating EU/EEA laboratories. The main residual gap concerns completion and harmonisation of serotype reporting from non-culture material. Recommended next steps include continued regular EQA rounds, targeted feedback to participants, improved collection of methodological information for non-culture pneumococcal workflows, continued support for standardised MIC reporting, and further harmonisation of WGSderived outputs.