SNP-based phylogenetic analysis of Mycobacterium tuberculosis strains in the Çukurova Region

Tuberculosis remains one of the most significant infectious diseases worldwide, and its causative agent, the Mycobacterium tuberculosis(MTBC), undergoes various mutations over time despite its high genetic stability. Among these mutations, single nucleotide polymorphisms (SNPs) may have decisive effects on the bacterial virulence mechanisms. SNPs can occur as insertions, deletions, or substitutions, and may influence the pathogen's biology by altering protein structure, gene expression, or regulatory pathways. In this study, we aimed to investigate the presence of SNPs in the mce1R, mce1A, yrbE1A, yrbE1A, phoP, and phoR gene regions—predicted to be associated with virulence—in M. tuberculosis strains isolated from the Çukurova Region that are resistant to at least one anti-tuberculosis drug, and to examine possible phylogenetic relationships among these strains. For this purpose, DNA sequence analysis was performed. According to the NCBI database, comparison of these genes in the H37Rv and H37Ra reference strains revealed a single transversion (C→T) at one site in the phoP gene, where all our clinical isolates showed the same sequence as the virulent H37Rv strain. In the phoR gene, the C nucleotide at position 852910 in the H37Rv reference strain was replaced by T in all clinical samples. Moreover, various SNPs were detected across all gene regions, particularly in the yrbE1A gene, in different clinical isolates. In conclusion, the SNP analyses conducted on the mce1 gene cluster and the phoPR system within the scope of this thesis provided preliminary evidence that these different SNP types insertions, deletions, and substitutions may influence the virulence mechanisms of M. tuberculosis.