M. leprae does not have a well-characterized DNA repair and damage tolerance machinery that is needed for survival and maintaining the structural integrity of the genome against DNA damaging agents [1,2]. Studying cellular processes, particularly those related to DNA repair pathways are typically difficult and the role of most of the DNA repair proteins is still not known due to the lack of culture medium for growth in M. leprae. It has been known that mutations that occur in the mycobacterial genome have a role in the development of antibiotic resistance [3]. Antibiotic exposure, oxidative and reductive stress, as well as a variety of other conditions that bacteria experience in the host, can all cause mutations in bacteria [4]. A base excision repair route is one of the several DNA repair pathways that bacteria use to help repair the damaged genome [5,6]. Previous studies have reported that drug resistance is evolving at a rapid rate in M. leprae [[7], [8], [9]]. The study of DNA repair pathways, particularly the base excision repair (BER) pathway, which removes damaged bases, is gaining popularity. The BER system is responsible for detecting and repairing DNA single-strand breaks, as well as acts on mutations caused by oxidative DNA damage such as 8-oxo-7,8-dihydroguanine (8-oxoG). The BER action begins with the excision of damaged bases by specialized enzymes called DNA glycosylases. The superfamilies of Uracil-DNA glycosylase, Fpg/Nei and Nth are the three primary DNA glycosylases found in E. coli [10]. Comparative genomic analysis of M. leprae TN genome with M. tuberculosis and E. coli has revealed that M. leprae lacks Fpg/Nei family genes and only has a single homolog of the endonuclease III gene [1].

A key component of the BER system is the nth gene which targets non-alkaline apurinic/apyrimidinic (AP) lesions, by cleaving the C–O–P bond which is on 3’ to the AP site, thereby leaving a gap with a 3-terminal unsaturated sugar and a 5-end phosphate, and then treat the gap with repair enzymes to finally remove the lesion. A change in the expression of the nth gene has a proven effect on the survival rate and drug resistance, such as in M. tuberculosis [11,12]. It was found that microbial organisms lacking the nth gene had slightly higher spontaneous mutation rates and were more susceptible to dying from oxidative stress than the wild-type strain [[13], [14], [15]]. In addition, nonsense mutations in the nth excision repair gene also increased sequence diversity and drug resistance [11,16,17].

In the case of mycobacteria, it has been found that the Nth and Nei deletion mutant demonstrates an exacerbated fall in survival rate and elevated rates of mutation in the presence of rifampicin [11]. Similarly, in a recent study, the nth gene of Campylobacter jejuni (cj0595c) was investigated for endonuclease III activity and its significance in preserving genomic integrity. The results revealed that in comparison to the wild-type strain, inactivation of nth has been associated with an increased frequency of spontaneous resistance mutation against fluoroquinolone-resistant and oxidative stress-resistant mutant strains of C. jejuni [18].

In the absence of DNA glycosylases Fpg/Nei in M. leprae, the Nth becomes one of the most important DNA glycosylases. Therefore, this study was purposed to analyze the point mutations within the nth gene region of M. leprae and explore its correlation between drug-sensitive and drug-resistant M. leprae clinical samples through Polymerase Chain Reaction (PCR) and Sanger sequencing.