Pneumococcal serotypes in urban Ugandan children vaccinated with the 10-valent pneumococcal conjugate vaccine

Uganda introduced the PCV10 vaccine into routine infant immunization in 2014, but molecular data on residual vaccine-type carriage after introduction are limited. Here, we assessed pneumococcal carriage and vaccine-type serotype distribution among urban children aged ≤ 5 years, five years after PCV10 introduction, using real-time quantitative PCR (qPCR). In this retrospective laboratory analysis of stored samples, 156 bacterial isolates from 194 children (one per child) were subcultured and re-characterized, of which 90 were pneumococci. Of these, 71% (64/90) were confirmed by qPCR, corresponding to an overall carriage prevalence of 33% (64/194). qPCR analysis of the pneumococci for PCV10/PCV13-associated capsular targets identified 24/64 (38%) isolates, while 40/64 (63%) were untypeable. Among the qPCR-positive isolates, serotype 14 predominated (6/64, 9.4%), followed by serotype 19 A (5/64, 7.8%), and serotype/serogroups 3, 7 F/7A, and 9 V/9A (6.3% each, 4/64, as grouped qPCR targets); serogroup 18 C/18F/18A was associated with one isolate (1.6%, 1/64). In summary, PCV10-associated serotypes (i.e., 14, 7 F, 9 V, 18 C) can persist in vaccinated children for years after vaccination. However, because our assay did not distinguish among individual serogroups (i.e., for 7 F/7A, 9 V/9A, 18 C/18/F/18A), further studies are needed to validate these findings and assess their impact on pneumococcal carriage and control.