Penicillin-Binding Protein Typing, Antibiotic Resistance Gene Identification, and Molecular Phylogenetic Analysis of Meropenem-Resistant Streptococcus pneumoniae Serotype 19A-CC3111 Strains in Japan

Since the introduction of pneumococcal conjugate vaccines, the prevalence of non-meropenem-susceptible pneumococci has been increasing in Japan. In an earlier study, we demonstrated that multidrug-resistant serotype 15A-ST63 in Japan has a specific sequence ( -13) that could promote meropenem resistance. To trace the origin of , we analyzed isolates of serotype 19A-CC3111, which is the most prevalent non-meropenem-susceptible clone in Japan. We analyzed a total of 119 serotype 19A-CC3111 strains recovered in Japan using whole-genome sequencing. Of the 119 isolates, 53 (44.5%) harbored -13, indicating that the clone may be the primary reservoir of the type and that the region may be horizontally transferred between different serotype strains. The single acquisition of -13 seemed to cause only penicillin resistance and not multidrug resistance; a combination of penicillin-binding protein (PBP) recombination in the and/or region(s) with acquisition of -13 caused multidrug resistance. Conserved amino acid motif analysis suggested that the 370SXXK, 448SXN, and 337SXXN motifs were the candidates for amino acid substitutions increasing the MICs of meropenem, cefotaxime, and penicillin. We identified a specific clone that was correlated with multidrug resistance, although no correlation was observed between phylogenetic trees generated using core genomes and those generated with only the locus. All tested isolates were highly erythromycin resistant, and most harbored within macrolide efflux genetic assembly (MEGA) elements and within Tn , which was inserted within Tn and exhibited a structure identical to that of Tn .