Sequence Variation Analysis of cpsA and cpsB Genes in Different Serotypes of Streptococcus pneumoniae

Turumugon, Hagilan (2021) Sequence Variation Analysis of cpsA and cpsB Genes in Different Serotypes of Streptococcus pneumoniae. [Project Paper] (Submitted)

Text FPSK2 2021 27.pdf Download (3MB)

Abstract

Pneumonia has been the second cause of death in Malaysia in past years. In 2017, over 800,000 children worldwide under the age of 5 died due to pneumonia. Pneumonia is an infectious disease mainly caused by a pathogen called Streptococcus pneumoniae. The polysaccharide capsule (cps) produced by this pathogen is a major virulence factor that allows pneumococcus to escape the host immune system, and capsular structural and antigenic variations distinguish S. pneumoniae into more than 95 serotypes. The sequences of the cps genes differ between pneumococcus serotypes; however, the highly conserved regulatory genes, cpsA and cpsB, were the focus of this study. The cpsA gene can distinguish between Streptococcus species, whereas the cpsB gene can distinguish between Streptococcus pneumoniae serotypes. Objective: This study aims to determine sequence variations in cpsA and cpsB genes and the evolution of Streptococcus pneumoniae through phylogenetic trees. Methodology: Sequences of CPS genes from different countries were extracted from National Center for Biotechnology Information (NCBI) Genbank. Individual sequences that code for cps genes were identified and collected from the long sequences extracted from the NCBI database. Then, each individual sequence of cpsA and cpsB genes were analysed for variation using bioinformatic tools (e..g clustalW). Lastly, a phylogenetic tree was constructed using Molecular Evolutionary Genetics Analysis (MEGA 7) software to study the evolutionary pattern of the genes in Streptococcus pneumoniae. Results: The multiple sequence alignment of cpsA gene sequences of S. pneumoniae are highly conserved with minor mutations in serotypes such as serotype 5, 6B, 7F and 18C. This study showed that each serotype has a distinct variation in the cpsB gene sequences of different S. pneumoniae isolated from different geographical regions, except there are no distinct variations in multiple sequence alignment of serotype 1. The phylogenetic analysis of cpsA and cpsB genes revealed the evolutionary relationships of different pneumococcal serotypes from different geographical regions. Discussion: Several factors cause variations in cps gene sequences of serotypes. This bioinformatic analysis provides a comprehensive summary of the distinct variations found in each serotype of S.pneumoniae. The multiple sequence alignment of cps genes of serotypes showed variations in the sequences caused by DNA mutations such as base substitutions, inversion, and deletions. It is believed that these variations are responsible for the invasiveness of each serotype and non-susceptibility to pneumococcal conjugate vaccines (PCV). Conclusion: This sequence variation analysis might provide an understanding of single gene sequetyping of Streptococcus pneumoniae and susceptibility towards PCV. However, further laboratory experimental validation needs to be done to verify these bioinformatic analyses.

Item Type:	Project Paper
Faculty:	Faculty of Medicine and Health Science
Depositing User:	Ms. Nor Safa'aton Saidin
Date Deposited:	22 Aug 2023 07:54
Last Modified:	22 Aug 2023 07:54
URI:	http://psaspb.upm.edu.my/id/eprint/1122

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