Genomic features of pneumococcal strains isolated from paediatric patients with invasive disease during pneumococcal conjugate vaccine introduction in Lima, Peru

To determine changes in the pneumococcal serotypes, sequence types (STs), clonal complexes (CCs) and the frequency of antimicrobial resistance genes after the introduction of pneumococcal conjugate vaccines (PCVs) in Lima, Peru. Retrospective multicentre study analysing whole-genome sequencing (WGS) data from three passive surveillance studies of invasive pneumococcal disease (IPD) in paediatric patients in Lima (2006-2020). Pneumococcal typing and antimicrobial resistance were analysed using <i>in silico</i> genomic tools. CCs were identified with eBURST and phylogenetic results were visualized using PHYLOViZ. 262 pneumococcal isolates were analysed (104 from IPD1, 70 from IPD2 and 88 from IPD3), 55.3% from children under 2 years old, 53.1% from patients with pneumonia and 28.5% with meningitis. After the introduction of PCVs, vaccine serotypes decreased, while serotype 19A and non-vaccine serotypes increased. The predominant STs were ST156 in IPD1 (<i>n</i>=25) and in IPD2 (<i>n</i>=7); and ST320 (<i>n</i>=38) and ST230 (<i>n</i>=15) in IPD3. Sixteen CC were identified, the most frequent were CC1421 (<i>n</i>=58) and CC156 (<i>n</i>=36). The overall penicillin non-susceptibility (NS) increased from 21.8% in IPD1 to 28.6% in IPD3, ceftriaxone-NS increased from 10% to 13.1% and macrolide-NS from 24.8% to 85.7% respectively. Resistance markers for macrolides, tetracycline and cotrimoxazole increased post-PCV13. WGS predicted antimicrobial resistance with high concordance, though some discrepancies were noted with phenotypic testing methods. Important changes in the distribution of serotype and ST, especially among vaccine serotypes, have been observed. These findings highlight the importance of monitoring vaccine effectiveness and tracking changes in bacterial populations to guide future vaccine implementation.