Prediction of genes encoding toxin of Mycobacterium tuberculosis H37RV strain

Abstract Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis, primarily affects the lungs but can spread to other organs. It is a major global health issue, leading to nearly 2 million deaths annually. Early diagnosis is vital for effective treatment, yet traditional methods like culture and smear microscopy can take 6–8 weeks. This highlights the need for molecular diagnostics that can rapidly detect TB DNA. Therefore, the present study aims to predict genes encoding toxins in the M.tuberculosis strain H37Rv, widely used in tuberculosis research. For this purpose, a total of one whole genome sequence of M. tuberculosis strain H37Rv was retrieved from NCBI, and the 16s RNA, MGE, resistance genes, toxin-encoding genes, and proteins associated with the toxin genes were analyzed using; NCBI, ContEst16S, Rapid Annotation Search Tool (RAST), Rapid Annotation using Subsystem Technology (RAST) quality report and TubercuList website. This finding identified 47 16S rRNA genes and 59 toxin-encoding genes associated with various toxin proteins. We assessed genome similarities and Average Nucleotide Identity (ANI) among toxin genes. Notably, except for two toxin genes, all other sequences showed a 0.00% OrthoANI value. Additionally, antibiotic resistance genes identified include gidB, gyrA, gyrB, rpoB, rpsL, rrs, inhA, embB, katG, and pncA, with the latter four being specific to M. tuberculosis. The results of this study also revealed homologs of VapC toxins in M.tuberculosis, linked to VapBC toxin-antitoxin systems. These findings lay the groundwork for future research on toxin-encoding genes and antibiotic resistance in M.tuberculosis H37Rv.