Introduction: To determine the phenotypes and genotypes of invasive Streptococcus pneumoniae  (S. pneumoniae ), 108 strains were isolated from paediatric patients with invasive pneumococcal diseases (IPDs) in Shenzhen from 2014 to 2018.
Methods: Serotype profiles were defined by multiplex PCR of the capsule gene. Pneumococcal surface protein A (PspA) classification was performed through pspA  gene sequencing. Antimicrobial resistance was examined by broth microdilution. Multilocus sequence typing (MLST) was determined based on next-generation sequencing data.
Results: Eighty-one S. pneumoniae  of 17 serotypes were finally collected. The coverage of the 13-conjugated polysaccharide vaccine (PCV13) was 88.9%. After the introduction of PCV13, the nonvaccine serotypes were added by serotypes 15b, 16F and 20. Vaccine serotype 3 increased by four serious cases. The pspA family 1 and pspA family 2 are predominant. The multiple drug resistance rate is 91.3%. None of the nonmeningitis isolates were resistant to penicillin, while 98.8% of all the isolates were resistant to erythromycin.
Discussion: This work characterizes the molecular epidemiology of invasive S. pneumoniae  in Shenzhen. Continued surveillance of serotype distribution and antimicrobial susceptibility is necessary to alert antibiotic-resistant nonvaccine serotypes and highly virulent serotypes.
Keywords: Streptococcus pneumoniae , invasive pneumococcal disease, PspA family, serotype, antimicrobial resistance