Assessment of the local clonal spread of Streptococcus pneumoniae serotype 12F caused invasive pneumococcal diseases among children and adults

Abstract

Background: We conducted active surveillance to elucidate the distribution of Streptococcus pneumoniae serotypes causing invasive pneumococcal disease (IPD) and clarified the genetic relatedness among the isolates in Kobe City, Japan. Methods: Forty-five IPD-causing S. pneumoniae strains were analyzed from March 2016 to May 2018 through active surveillance in Kobe City, Hyogo, Japan. Serotypes were determined by multiplex serotyping PCR and the Quellung reaction with pneumococcal antisera. Fourteen Sp12F strains were subjected to whole-genome sequencing (WGS). Results: Among 45 isolates, the most frequent serotypes were 12F (n = 14, 31%), 24F (n = 5, 11%), and 10A (n = 4, 9%). Multilocus sequence typing (MLST) analysis of 14 isolates of Sp12F divided them into ST4846 (n = 4) and ST6495 (n = 10). WGS showed clonality of the 10 isolates of ST6495, with only 13 single nucleotide polymorphisms in the genomes. Meanwhile, ST4846 strains in Kobe differed from only the outbreak strains of Sp12F ST4846 in Tsuruoka, Japan, reported on 2018. Conclusions: Serotype monitoring showed Sp12F to be the predominant serotype in Kobe, and WGS revealed the clonal spread of Sp12F ST6495 in this city. Thus, the spread of Sp12F could become a serious public health problem in Japan, warranting thorough monitoring in future. Keywords: Streptococcus pneumoniae, Serotype, Sp12F, Whole-genome sequencing, Single nucleotide polymorphism