Comparative Genomic Analysis of Clinical Streptococcus Pneumoniae Isolates Reveal 31 New Unique Drug Resistant SNPs Using Whole Genome Sequencing

Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing. Abstract Streptococcus pneumoniae is the leading cause of respiratory infections worldwide, specifically community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. In this study, we performed whole genome sequencing (WGS) for ten pneumococcal clinical isolates with different levels of antibiotic resistance. The key objective is to investigate genetic changes associated with antibiotic resistance in S. pneumoniae . Our results showed that resistant isolates contain higher non-synonymous single nucleotide polymorphisms (SNPs) within genes coding for virulence factors as compared to susceptible isolates, suggesting that drug resistance is essentially determined by the occurrence of SNPs rather than the presence or absence of virulent genes. In addition, 90 SNPs were identified that were unique to resistant isolates. Out of these 90 SNPs, 31 were unique and have not been reported previously. Detection of SNPs associated with antibiotic resistance is crucial for the future use of genome sequencing to predict antibiotic susceptibility in clinical microbiology and for developing new anti-pneumococcal drugs.