DESAIN PRIMER SECARA IN SILICO UNTUK AMPLIFIKASI GEN phtD BAKTERI STREPTOCOCCUS PNEUMONIAE

Abstract

Background: Pneumonia remains an infectious disease that is commonly suffered by vulnerable groups, namely children under five years of age and the elderly. Pneumonia is caused by the bacterium Streptococcus pneumoniae. The mortality and morbidity rates of pneumonia infection are very high. S. pneumoniae has a phtD gene that plays a role in host cell adhesion, so it is often associated with bacterial virulence. Its ability to trigger immunity makes phtD a candidate for a vaccine because of its immunogenic properties. The development of specific biomarkers is a priority to improve the quality of laboratory services to prevent and accelerate treatment. Specific primer designs are needed for PCR molecular testing. Methods: This study used a literature review from the NCBI gene bank to obtain the phtD gene sequence of S. pneumoniae bacteria with access number KP127708.1. The gene sequence was analyzed using Primer BLAST, and then each primer obtained was identified according to the criteria for a good primer. Results: From the 10 candidate primers obtained, analyses were conducted on GC content, primer length, and the presence or absence of hairpins and dimers. The results of the analysis with these criteria referred to primer pair number 2. Then, a specificity test was carried out on the S. pneumoniae species, and the gene homology level in the species group in the BLAST test lso showed 100% attachment to that species. Conclusion: forward primer F5 ‘TGGCAGGCAAGTACACAACA3’ and reverse primer R3 ‘GCCTCCGCATCTGCTATCTT5’.