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<i>Streptococcus pneumoniae</i> is one of the most common bacterial pathogens of a wide range of community-acquired infections. It has been more and more recognized that this bacterium could also play a role as a cause of nosocomial infections. In this study, by retrospective analysis of the phenotypic resistance characteristics and genomic characteristics of 52 <i>S. pneumoniae</i> isolates in a hospital in Beijing, China, from 2018 to 2022, we explored the carriage of resistance genes and mutations in penicillin-binding proteins corresponding to the resistances, and identified the population diversity based on the prediction of serotypes and identification of sequence types (STs). The isolates displayed resistances to erythromycin (98%), tetracycline (96%), sulfonamide (72%) and penicillin G (42%). Among the 52 isolates, 41 displayed multiple-drug resistance. In total, 37 STs and 21 serotypes were identified, and the clonal complex 271 serogroup 19 was the most prevalent subtype. Only 24 isolates (46.2%) of 7 serotypes were covered by the 13-valent pneumococcal conjugate vaccination. The isolates showed high carriages of resistance genes, including <i>tet</i>(M) (100%) and <i>erm</i>(B) (98.1%); additionally, 32 isolates (61.5%) had mutations in penicillin-binding proteins. We also observed 11 healthcare-associated infections and 3 cases infected by different subtypes of isolates. We did not find nosocomial transmissions between the patients, and these cases might be associated with the asymptomatic colonization of <i>S. pneumoniae</i> in the human population. Our results called for further active surveillance of these subtypes, as well as the continuous optimization of the treatment protocols.