South Asian Journal of Research in Microbiology

Streptococcus pneumoniae remains a major cause of childhood morbidity and mortality globally, particularly in sub-Saharan Africa. Nasopharyngeal carriage in children is a precursor for invasive pneumococcal disease and serves as a reservoir for community transmission. Although pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal disease, their effect on local carriage patterns in Nigerian communities remains underexplored. This study evaluated the impact of PCV immunisation on nasopharyngeal carriage of S. pneumoniae among children aged 0-5 years in Khana Local Government Area (LGA), Rivers State, Nigeria. A cross-sectional study was conducted among 200 preschool children recruited across ten communities in Khana LGA. Sociodemographic and vaccination information was collected using interviewer-guided questionnaires. Nasopharyngeal swabs were cultured on chocolate and blood agar, and isolates were identified using Gram staining and standard biochemical tests. Antimicrobial susceptibility testing was performed on recovered isolates. In addition, molecular testing (PCR) was conducted on 30 (15.0%) nasopharyngeal samples for pneumococcal gene detection. No S. pneumoniae carriage was detected by culture, and PCR similarly yielded no positive cases. In contrast, Staphylococcus spp. were identified in 43.0% of participants, with carriage differing significantly by location (p = 0.0005) but not by age, sex, school type, PCV immunisation status, or months since last antibiotic use. The antimicrobial susceptibility profile of Staphylococcus isolates showed the highest resistance to amoxicillin-clavulanic acid, cefepime, and clindamycin, each at 46.5%, with cefoxitin resistance in 32.6% and cefuroxime resistance in 19.8%. No resistance was detected to cefotaxime, meropenem, vancomycin, or erythromycin, while levofloxacin resistance was 1.2%. Pneumococcal carriage was not detected in this population by either culture or molecular methods, suggesting very low or absent carriage in the study setting, while highlighting substantial Staphylococcus carriage and noteworthy resistance to several commonly used antibiotics.