Volledige genoomsequentie bepaling van Streptococcus pneumoniae om opkomende serotypes en antimicrobiële resistentie te karakteriseren

The global implementation of pneumococcal conjugate vaccines (PCVs) has reshaped the epidemiology of invasive pneumococcal disease (IPD), creating a dynamic landscape defined by serotype replacement. This doctoral thesis addresses the added value to integrate whole-genome sequencing (WGS) into public health surveillance for prediction of antimicrobial susceptibility and in-depth investigation of epidemiological patterns in (vaccine) serotypes, clones or sequence types, supported by phylogenetic reconstruction and virulence factor gene analyses. In the context of this thesis, the resurgence of PCV serotype 4 IPD, a threat now concentrated primarily in vulnerable adult populations, was a main focus. This research pursued to answer three main objectives: First, the ability and diagnostic accuracy of bioinformatic tools that use WGS information to predict antimicrobial susceptibility of IPD isolates (Chapter 1). The evaluation of two prediction tools demonstrated high concordance with phenotypic AST methods, confirming WGS's feasibility to be implemented in the future as unified molecular pipeline in National Reference Centres (NRCs). Second, we performed an epidemiological and molecular characterisation of the serotype 4 surge in Belgium (Chapter 2). Analysis of epidemiological data since 2007 revealed that the accelerated resurgence, commencing around 2021, was heavily concentrated in socio-demographically vulnerable young adult males (18-49 years old) residing in urban centres, exhibiting high rates of unemployment, housing instability, and substance use. Crucially, the risk factors identified in this study have been considered for new recommendations/guidelines for adult pneumococcal vaccination in Belgium by the Superior Health Council, underscoring the immediate public health relevance of this research. The third phase involved a high-resolution transnational phylogenetic analysis of over 900 serotype 4 S. pneumoniae isolates from Belgium, England, and the Netherlands (Chapter 3). This comprehensive study showed that the resurgence - that is observed across the three nations - is not caused by the spread of a single clone, but instead by multiple, geographically independent lineages that seem to have expanded from the highly adapted GPSC 162. Molecular evidence highlighted critical adaptive strategies used by this emergent lineage: (i) local adaptation: Belgian clades I and VII showed a unique, conserved virulence factor profile with high co-prevalence of pspC and lytB. This suggests an optimised fitness suited to local transmission and host factors, though it must be noted that this VF analysis is preliminary and requires dedicated functional studies for definitive conclusions on causation and mechanism. (ii) Geographic divergence, phylogenetic clustering was country-specific primarily, driven by local clonal expansion within distinct sub-lineages. This expansion was linked across borders by limited international transmission signals, rather than a singular mass spread. In conclusion, this thesis validates WGS using a large Belgian dataset (>538 genomes), as the foundational tool required for integrated pneumococcal surveillance. The serotype 4 resurgence is defined as a socio-ecological event (in Belgium) rooted in the multi-clade expansion of a highly adapted lineage that exploits the immunological gap in vulnerable adults (in Belgium). These findings call for a change in public health policy, emphasising risk-factor-based vaccination screening and highlighting the vital role of integrating high-resolution genomic data