A genomic analysis of Mycobacterium immunogenum strain CD11_6 and its potential role in the activation of T cells against Mycobacterium tuberculosis

Abstract

Background: Mycobacterium tuberculosis (Mtb) is an etiological agent of tuberculosis (TB). Tuberculosis is a mounting problem worldwide. The only available vaccine BCG protects the childhood but not adulthood form of TB. Therefore, efforts are made continuously to improve the efficacy of BCG by supplementing it with other therapies. Consequently, we explored the possibility of employing Mycobacterium immunogenum (Mi) to improve BCG potential to protect against Mtb. Results: We report here the genome mining, comparative genomics, immunological and protection studies employing strain CD11_6 of Mi. Mycobacterium immunogenum was isolated from duodenal mucosa of a celiac disease patient. The strain was whole genome sequenced and annotated for identification of virulent genes and other traits that may make it suitable as a potential vaccine candidate. Virulence profile of Mi was mapped and compared with two other reference genomes i.e. virulent Mtb strain H37Rv and vaccine strain Mycobacterium bovis (Mb) AFF2122/97. This comparative analysis revealed that Mi is less virulent, as compared to Mb and Mtb, and contains comparable number of genes encoding for the antigenic proteins that predict it as a probable vaccine candidate. Interestingly, the animals vaccinated with Mi showed significant augmentation in the generation of memory T cells and reduction in the Mtb burden. Conclusion: The study signifies that Mi has a potential to protect against Mtb and therefore can be a future vaccine candidate against TB. Background: The treatment and control of tuberculosis (TB) is a growing challenge worldwide due to emerging multi-drug resistant strains of Mycobacterium tuberculosis (Mtb), failure of BCG vaccine and AIDS pandemic. BCG is a controversial vaccine since its protective efficacy varies from 0 to 85% [1,2,3]. Although, maximum number of people have been vaccinated with BCG worldwide, yet TB continues to afflict the global population. The vaccine protects the childhood but not adulthood manifestation of the disease. Extensive clinical trials conducted at Chengalpattu, Tamil Nadu, India suggested that BCG failed to protect TB-endemic population [4, 5]. Development of a safe and efficacious vaccine against TB has been recognized as an immediate global priority by the WHO. Alternative TB vaccines based on a BCG platform, or novel approaches to supplement BCG with agents that could enhance its efficacy, could be useful to combat TB in future. One of the many reasons for the failure of BCG vaccine is its inability to generate CD8 T cell response and to elicit long-lasting memory T cells [6, 7]. The earliest principles of vaccinology involves use of attenuated pathogens to allow its safe administration. Killed whole-cell mycobacterial vaccines may be a potential strategy for successful TB vaccine development. Seventy years ago, inactivated whole-cell mycobacterial vaccines administered in multiple-doses have shown protective efficacy in experimental models, as well as humans, but were not developed further after the discovery of BCG [8]. A prominent example is Mycobacterium vaccae (‘Vaccae’), a heat-inactivated whole-cell vaccine against TB, which is already being approved in China for the adjunct treatment of TB [9]. Mycobacterium immunogenum (Mi) is a non-tuberculous mycobacterium that is associated with hypersensitivity pneumonitis (HP). We did not observe any report demonstrating the role of Mi in protection against Mtb. The Mi strain CD11_6 was isolated from duodenal mucosa of a celiac disease (CD) patient. The strain was sequenced for determining its probable role in pathogenesis of CD, as microbes are known to play an important role in celiac autoimmunity [10,11,12,13,14]. The genomic annotations of Mi indicates that it possesses fewer virulence genes, as compared to BCG and target organism Mtb. Further, our in-silico studies indicate that it has sufficient antigenic repertoire; suggesting that it has enough potential to protect against Mtb. Sequence of Mi suggested that 16 out of total 26 peptides from Mtb showed sequence homology ranging 57–100% with similar cell surface proteins or secretory proteins of CD11_6 (Mi). Further, prior published literature suggests a probable role of Mi in eliciting immune response [15, 16]. This preliminary information had derived our interest to explore protective efficacy of Mi against Mtb. Keeping in view of above mentioned facts, we adjudged to use heat killed Mi as a vaccine candidate and check its efficacy against Mtb. The present study indicates that Mi can induce optimum activation of both CD4 T cells and CD8 T cells. Further, enhancement in the pool of memory T cells was noticed, as indicated by modulation in the expression of the memory markers CD44, CD127 and CD62L. Consequently, this signifies a possible use of Mi as a vaccine candidate against Mtb.