Are there any differences between genomic composition of clinical strains of Mycobacterium tuberculosis with H37Rv

Aims & objectives: The basis of antibiotic resistance in Mycobacterium tuberculosis (MTB), unlike Enterobacteriaceae, is the mutation in its chromosomal genes such as katG (Gene ID: 885638, causes isoniazid resistance) and rpoB (Gene ID: 888164, rifampin resistance). Evaluation of whole genome sequence of the standard strains of H37Rv in gene bank revealed the absence of integrons, plasmids and transposons. There are few reports on these genetic elements in clinical strains of MTB isolated from the patients. In this study, as a hypothesis based on the genetic composition differences between H37Rv and clinical isolates, and probably geographic differences between clinical strains genomic, we designed a study on a probably presence of a few genes in Iranian clinical strains. Methods: Previous studies of our research group showed that there is a new fragment in our clinical strains of MTB that was first recorded in the GenBank (Accession: MF279142.1). During extensive bioinformatics and gene bank (insilico) studies, it was found that this fragment might be a part of an integrase, belonging to a probably integron, plasmid, phage or transposon inside or outside the chromosome. Existence of its complete gene in different coding sequences was carefully investigated. A few genes including kleE, pmaB, sul, and suf, surrounding this fragment were amplified by using Mycobacterium abscessus plasmid and other non-tuberculosis mycobacteria as templets by PCR. Specific primers based on the aforementioned strains were designed. PCR reactions were optimized with various amplification programs. Bands were purified and were sequenced by ABI system apparatus. Sequencing results were analyzed by Mega, Chromas, and Basic Local Alignment Search Tool programs. Results: Bioinformatics analysis of sequencing results of purified 463bp amplicon revealed that the studied fragment was belonging to gene encoding dihydropterate synthase of Mycobacterium fortuitum but not in H37Rv and the other MTB strains in Gene Bank. It was confirmed that this new fragment there are in 30% of our clinical MTB strains. Conclusion: As the results, presence of a part of suf gene was reported for the first time in clinical isolates of Mycobacterium tuberculosis. Further experiences are under investigation to find the complete gene, and to examine whether it belongs to a larger genetic structure.