Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae in paediatric patients in Japan (2020– 2023)

Abstract

Introduction. Streptococcus pneumoniae remains a major pathogen causing invasive diseases in children worldwide. Although pneumococcal conjugate vaccines (PCVs) have significantly reduced the disease burden, non-vaccine serotypes and antimicrobial resistance continue to be of concern. Hypothesis/ Gap Statement. The epidemiology of paediatric invasive pneumococcal disease (IPD) and antimicrobial resistance patterns in Japan following the coronavirus disease 2019 pandemic and prior to the introduction of PCV15 and PCV20 has not been fully characterized. Aim. To investigate the recent distribution of pneumococcal serotypes, antimicrobial susceptibility and genetic characteristics of isolates derived from paediatric patients in Japan from 2020 to 2023. Methodology. We conducted a nationwide, prospective surveillance study from March 2020 to April 2023. A total of 151 pneumococcal isolates (126 from IPD cases and 25 from non-IPD cases) were collected from children under 15 years of age. Serotyping, antimicrobial susceptibility testing and whole-genome sequencing were performed to assess epidemiological and genomic features. Results. No patient mortality was reported, but sequelae were observed in 4 (3.2%) of 125 IPD patients. The most common serotypes in IPD were 15B/C (23.0%), 15A (11.1%) and 24B (10.3%). Among 126 IPD isolates, the vaccine coverage rates for PCV13, 15 and 20 were 0.8, 13.5 and 42.1%, respectively. Overall resistance rates to penicillin (PEN), cefotaxime, meropenem (MEM) and erythromycin (ERY) were 31.8, 15.9, 18.5 and 88.7%, respectively. Serotypes 15A-CC63 and 35B-CC558 showed high resistance rates to β-lactams, including MEM. Genomic analysis revealed that the predominant genotypes were 15B/C-CC199, 15A-CC63, 24B-CC2754 and 10A-CC5236. Conclusion. Non-vaccine and PEN-, MEM-and ERY-resistant clones, particularly 15A-CC63 and 35B-CC558, were prevalent among paediatric pneumococci in Japan. Even with PCV20, less than half of the IPD isolates were covered; this underscores the need for ongoing genomic surveillance, antimicrobial stewardship and consideration of expanded-valency vaccines targeting additional serotypes, such as 15A and 35B.