Serotype distribution and antimicrobial susceptibility patterns of Streptococcus pneumoniae isolates in the post–pneumococcal conjugate vaccine era in Nigeria: a hospital-based cross-sectional study

Pneumococcal conjugate vaccines (PCV7/10/13) have reduced vaccine-serotype disease and resistance globally, including indirect effects in unvaccinated populations. Nigeria introduced PCV10 in 2016, but its impact on serotype distribution and resistance in Delta State remains poorly defined. To determine the prevalence of Streptococcus pneumoniae, the circulating serotypes, and their antimicrobial susceptibility patterns among children and adults ~ 3 years post PCV10 introduction in Delta State, Nigeria. We processed 622 clinical specimens (July 2019–November 2020) from two hospitals. Isolates with α-hemolysis and optochin susceptibility were confirmed as pneumococci by multiplex PCR targeting cpsA. Serotyping used a multiplex PCR panel covering PCV13 serotypes. Antimicrobial susceptibility testing was by Kirby–Bauer disk diffusion; S/I/R (Susceptibility/Intermediate/Resistance) categories were assigned only for agents with validated disk-diffusion breakpoints in S. pneumoniae (erythromycin, clindamycin, tetracycline, levofloxacin, trimethoprim–sulfamethoxazole). Because neither oxacillin screening nor MIC testing was performed, β-lactams, imipenem, and vancomycin were reported as inhibition-zone diameters without categorical interpretation. Of 622 specimens, 8 (1.3%) yielded phenotypic pneumococci; 5/8 (62.5%) were cpsA-positive, all from non-invasive specimens. By age, 3/5 (60%) were from adults ≥ 61 years, and 1/5 each from 11 to 20 and 21–40 years. All five isolates were non-vaccine types (non-PCV13); specific serotypes were not resolved. Among drugs with validated disk-diffusion breakpoints, 4/5 (80%) isolates were susceptible to erythromycin, clindamycin, and levofloxacin; all 5/5 (100%) were non-susceptible to trimethoprim–sulfamethoxazole; and 3/5 (60%) were non-susceptible to tetracycline. Using a non-β-lactam definition, multidrug resistance (MDR) was detected in 1/5 (20%) isolates. In this two-site survey, pneumococci were infrequently recovered and comprised non-vaccine types that largely retained susceptibility to macrolide, lincosamide, and fluoroquinolone agents, alongside uniform non-susceptibility to trimethoprim–sulfamethoxazole and sporadic MDR. Although numbers are small, these findings support continued serotype-specific and resistance surveillance incorporating MIC testing and molecular typing to track serotype replacement, clarify resistance mechanisms, and evaluate the longer-term impact of PCV10 in Delta State, Nigeria.