Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates

Streptococcus pneumoniae can cause several diseases including otitis media, sinusitis, pneumonia, sepsis and meningitis. The introduction of pneumococcal vaccines has changed the molecular epidemiological and antibiotic resistance profiles of related diseases. Analysis of molecular patterns and genome sequences of clinical strains may facilitate the identification of novel drug resistance mechanism. Three multidrug resistance 19A isolates were verified, serotyped and the complete genomes were sequenced combining the Pacific Biosciences and the Illumina Miseq platform. Genomic annotation revealed that similar central networks were found in the clinical isolates, and Mauve alignments indicated high similarity between different strains. The pan-genome analysis showed the shared and unique cluster in the strains. Mobile elements were predicted in the isolates including prophages and CRISPER systems, which may participate in the virulence and antibiotic resistance of the strains. The presence of 31 virulence factor genes was predicted from other pathogens for PRSP 19339 and 19343, while 30 for PRSP 19087. Meanwhile, 33 genes antibiotic resistance genes were predicted including antibiotic resistance genes, antibiotic-target genes and antibiotic biosynthesis genes. Further analysis of the antibiotic resistance genes revealed new mutations in the isolates. By comparative genomic analysis, we contributed to the understanding of resistance mechanism of the clinical isolates with other serotype strains, which could facilitate the concrete drug resistance mechanism study.