P089

1:National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; 2:Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal

Portugal is a medium incidence tuberculosis (TB) country, with 14.9 cases per 100 000 inhabitants reported in 2023. In an effort to improve TB surveillance and diagnosis, the Portuguese National Reference Laboratory (NRL) began implementing whole-genome sequencing (WGS) for all RR/MDR-TB cases in 2019. Since 2020, this approach has been expanded to include all isolates received by the NRL, and has undergone upgrades towards antimicrobial resistance (AMR) prediction and epidemiological analysis.

Here we aim to describe our current WGS-based surveillance system, which relies on three main steps: QC/QA and contamination assessment, with a novel data filtering step (Kraken_v2); genotyping and AMR prediction (tb-profiler_v6 plus WHO 2024 catalogue); and dynamic SNP-based approach, that maximizes the number of variable sites under analysis (Reportree_v2). Among the pipeline upgrades, we highlight: i) the novel filtering step that allowed the improvement of 111 out of 147 contaminated samples, reducing false positive results in AMR typing, without hampering SNP-based analysis; ii) the inclusion of 5% missing data per site threshold (Reportree) which more than doubled the resolution of the core variable sites under analysis (~40000 vs 20000 sites for 100% core-SNPs); iii)  the automatic maximization of the number of shared variable sites (zoom-in/Reportree) for in-depth cluster analysis, which is key to consolidate genetic links for epidemiological investigation. The advantages of these novel features will be presented in light of data from the last five years (n=869) framed with retrospective data (n=302). Ultimately, the implemented system has significantly contributed towards strengthening TB surveillance and diagnosis in Portugal.