Objective/Background: The incidence of resistant strains of Mycobacterium tuberculosis (MTB), including multi-drug resistant, extensively drug resistant, or totally drug resistant, is one of the major problems of health policies worldwide. The accumulation of mutations causes multi-drug resistant strains. Mycobacterium abscessus has a plasmid called pMab2401 containing the trfA1 gene in its integron part. The aim of the present study was to investigate the possible existence of the trfA1 gene in clinical strains of MTB for the first time. Methods: Bioinformatics analysis in GenBank revealed an absence of any integrons or internal components in MTB. Several specific primers for different genes and the trfA1 gene of M. abscessus were used in a touch-down (60–52) amplification program and followed by loading on gel electrophoresis. Products were extracted and were sequenced. Sequencing results were analyzed carefully and compared with those in the databank. Results: Bands of 500bp were resulted with pair primers in an amplification reaction by clinical MTB that has 94% identity with a fragment in most plasmids and phages M13. It should be noted that such an independent replication system-like structure has not been reported to date in MTB strains. Conclusion: The trfA1 gene is depends on the replication process. It is necessary to investigate other probable new areas that may be of concern with drug resistance in clinical isolates of MTB.