Pneumococcal carriage and selected respiratory virus in children with clinical pneumonia in Salvador, Brazil during PCV10 era

Background In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10 GSK ). Assessing pneumococcal carriage among children with clinical pneumonia in the context of a mature PCV10 GSK program can inform decisions about use of next-generation PCVs. Methods We prospectively enrolled children aged 2–59 months meeting a standardized case definition for clinical pneumonia at two emergency care units in Salvador, Brazil. Nasopharyngeal specimens were tested for pneumococcus by culture and qPCR with serotyping by Quellung and/or PCR or qPCR; isolates underwent antimicrobial susceptibility testing (AST). Respiratory viruses were detected using qPCR, and respiratory syncytial virus (RSV) strains were genotyped. Results From March 2023 to March 2024, 170 children with clinical pneumonia were enrolled; 93.5% were up to date on pneumococcal vaccination. Pneumococcal carriage was detected in 62.7% (106/169 swabbed patients; 55 by culture and 51 by qPCR). Among the 106 pneumococcal carriers, the most prevalent serotypes were 6C (18.9%), 11A/D (9.4%), 19A (7.5%), 3 (6.6%), 19F (5.7%), 6A (5.0%), and 23B (4.7%). PCV10 GSK serotypes (19F, 4, 7F/A, 9V/A, 23F) were detected in 10.4% (11/106) of pneumococcal isolates, driven by serotype 19F (5.6%). The proportions of carriers with serotypes including in PNEUMOSIL, 13, 15, and 20 serotypes, were 21.7%, 29.2%, 30.2%, and 40.6%, respectively. Among 53 isolates with AST, more than 30.0% were resistant to macrolides and 35.8% were penicillin non-susceptible. RSV was detected in 20.6% (35/170) of cases, predominantly RSV-A (72.0%); 60.0% of RSV-positive cases were colonized with pneumococcus. Conclusion More than a decade after PCV10 GSK introduction, and despite high vaccination coverage, PCV10 GSK serotypes remain detectable among pneumococci carried by children with pneumonia. Next-generation PCVs provide broader serotype coverage. Continued monitoring of the persistent circulation of vaccine serotypes remains important.