Genomic surveillance of post-immunization pneumococcal carriage in Ghana

Streptococcus pneumoniae remains a major cause of morbidity and mortality worldwide, especially among children under five years of age. The introduction of pneumococcal conjugate vaccines (PCVs) has significantly reduced invasive pneumococcal disease (IPD) globally. Ghana introduced routine immunization with PCV13 in 2012; however, its impact on pneumococcal carriage at the genomic level remains largely unexplored. This study aimed to assess changes in pneumococcal carriage among children in Ghana following the introduction of PCV13, focusing on shifts in sequence types (STs), Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance profiles through genomic surveillance. We identified substantial genomic diversity among carriage isolates, including 49 GPSCs and 67 STs, of which 21 STs were novel, and four were international PMEN clones (Spain9V-3, Greece6B-22, NorwayNT-42, and Sweden15A-25). GPSC 5 (14%) was the most prevalent cluster, followed by GPSC 20 (6%). GPSCs associated with antibiotic resistance (GPSC 1, 6, and 10) represented 2%, 3%, and 2% of isolates, respectively. Importantly, we observed a significant decline in vaccine serotypes (VT) and a corresponding rise in non-vaccine serotypes (NVT), notably serotypes 23B and 15BC. Additionally, vaccine serotypes demonstrated higher levels of antibiotic resistance compared to non-vaccine serotypes (p=0.05). This study provides the first genomic epidemiological insights into pneumococcal populations in Ghana post-PCV13 introduction and underscores the importance of continuous genomic surveillance to monitor serotype replacement and antibiotic resistance trends.