Antibiotic susceptibility testing and molecular characterization based on whole-genome sequencing of Streptococcus pneumoniae isolates from pediatric infections at the National Regional Medical Center of Southwest China during the COVID-19 pandemic

Background: Streptococcus pneumoniae is a transmitted respiratory pathogen that causes high morbidity and mortality in children, especially those under 5 years of age. During the implementation of population control measures for COVID-19 in mainland China, the Streptococcus pneumoniae detection rate in pediatric patients decreased. However, with the second wave of the COVID-19 pandemic (2022), the incidence of pneumococcal disease (PD) and even invasive pneumococcal disease (IPD) began to rise again.

Methods: This study was conducted from August 2022 to September 2023 at a national regional medical center based mainly in West China Second University Hospital, Sichuan University. The demographic and clinical characteristics of S. pneumoniae-infected pediatric patients were analyzed. All S. pneumoniae isolates were subjected to standardized clinical sample inoculation, culture, subculture, and identification procedures. Next-generation sequencing and analysis were used to determine serotypes and sequence types (STs) and evaluate antibiotic resistance- and virulence-related genes. Antimicrobial susceptibility was determined in AST dishes via the broth microdilution method.

Results: The prevalent serotypes in the IPD patients were 14, 6A, and 23F, and the prevalent serotypes in the NIPD patients were 19F and 6A. A significant difference in the proportion of patients with serotype 14 was noted between the two groups. A total of 23 STs were identified and classified into 13 different GPSC lineages, including 4 novel STs (ST18449, ST18451, ST18464 and ST18466) and 1 novel allele (ddl1209). According to the interpretation breakpoints for non-meningitis infections, the resistance/nonsusceptibility rates of invasive isolates were as follows: penicillin (0.0%/8.3%), amoxicillin (0.0%/0.0%), cefotaxime (8.3%/16.6%), ceftriaxone (8.3%/8.3%), and cefepime (0.0%/8.3%). The resistance/nonsusceptibility rates of invasive isolates according to the meningitis breakpoints were as follows: penicillin (100.0%), cefotaxime (16.7%/33.4%), ceftriaxone (8.3%/50.0%), and cefepime (8.3%/66.7%). All the isolates were susceptible to rifampicin, levofloxacin, moxifloxacin, linezolid and vancomycin. In addition, the characteristics of the antibiotic resistance-related genes and virulence genes of serotype 19F were significantly different from those of the other serotypes.

Conclusion: These data provide valuable information for understanding pediatric pneumococcal disease during the second outbreak of COVID-19 in Southwest China and will contribute to the prevention and treatment of S. pneumoniae infection.