Isolation of yidRhv Gene from Hypervirulent Klebsiella pneumoniae Indonesia Strain and in silico study of Gene product

Abstract

There is an increase rate of hypervirulent Klebsiella pneumoniae (hvKP) that urges the need for preventive and effective immunotherapies, such as vaccine. The YidR gene is a new gene for adherence to host that is conserved in many strain of Klebsiella sp, offering its potency as vaccine candidate. This study aims to isolate the YidRhv gene and analyze the YidRhv protein in silico for future work as vaccine candidate against hypervirulent K. pneumoniae Indonesia strain. Klebsiella pneunomiae is tested for hypervirulency using LAMP-PCR method. The YidRhv gene was amplified via PCR method and the fragment produced was cloned and sequenced. The protein structure and epitope prediction for T-cell and B-cell of YidRhv protein was analyzed using bioinformatics approach. DNA sequence of YidRhv gene strain consisted of 1227 base pairs and showed 99,75 % homology to yidR from classical K pneumoniae. However, several single nucleotide polymorphism were found in this gene. The protein structure demonstrated that the YidRhv is possibly outer membrane protein. The protein YidRhv contain predicted epitopes that showed high affinity to B-cell but low affinity to T-cell.