DOI: 10.6084/m9.figshare.30021733
title: Data for recombination and SNP analysis

description: <i>Streptococcus pneumoniae</i> is a leading cause of sight-threatening ocular infections. However, the comprehensive molecular epidemiology analysis focusing on ocular pneumococcus is limited. We performed high-resolution genomic ocular pneumococcal isolates from Zhejiang, China. Serotyping was performed by latex agglutination and Quellung reaction, and Illumina short-read data were assembled de novo. Meanwhile, we compiled a global dataset of 58 ocular <i>S. pneumoniae</i> genomes, subjected them to core-genome SNP calling, resistance-gene BLAST, recombination profiling, and SNP analysis. Nine serotypes were identified in our collection, with PCV13 covering 54.5%. One strain was resistant to PEN and CRO, and all strains were resistant to ERY and susceptible to LVX. Phylogenetic analysis revealed Chinese isolates showing a sporadic distribution. Antimicrobial resistance gene detection showed that all strains carry the <i>ermB</i> gene for macrolide resistance instead of <i>mefA</i> in strains from Western countries. The virulence gene analysis showed that no non-typeable (NT) strain was found for conjunctivitis, and no <i>zmpC</i> gene was identified in Chinese keratitis and conjunctivitis pneumococcal strains. The DNA integrity gene (<i>SP_1247</i>) was found to be critical for ocular pneumococcus worldwide. Streptococcus pneumoniae is a leading cause of sight-threatening ocular infections. However, the comprehensive molecular epidemiology analysis focusing on ocular pneumococcus is limited. We performed high-resolution genomic ocular pneumococcal isolates from Zhejiang, China. Serotyping was performed by latex agglutination and Quellung reaction, and Illumina short-read data were assembled de novo. Meanwhile, we compiled a global dataset of 58 ocular S. pneumoniae genomes, subjected them to core-genome SNP calling, resistance-gene BLAST, recombination profiling, and SNP analysis. Nine serotypes were identified in our collection, with PCV13 covering 54.5%. One strain was resistant to PEN and CRO, and all strains were resistant to ERY and susceptible to LVX. Phylogenetic analysis revealed Chinese isolates showing a sporadic distribution. Antimicrobial resistance gene detection showed that all strains carry the ermB gene for macrolide resistance instead of mefA in strains from Western countries. The virulence gene analysis showed that no non-typeable (NT) strain was found for conjunctivitis, and no zmpC gene was identified in Chinese keratitis and conjunctivitis pneumococcal strains. The DNA integrity gene (SP_1247) was found to be critical for ocular pneumococcus worldwide. Recombination analysis suggested significantly more SNPs and mosaic blocks in Asian strains, correlating with region-specific gains of the ATP-dependent protease SP_0338 and UV-damage repair uvrB alleles. Collectively, our high-resolution WGS analysis reveals that ocular pneumococci in China exhibit unique serotype coverage, ermB-driven macrolide resistance, and ocular environmental adaptation that should guide local vaccine updates, antibiotic choices, and molecular diagnostics to prevent the related infections.