<p>Abstract</p> <p>Background</p> <p>Tuberculosis is endemic to developing countries like India. Though the whole genome sequences of the type strain <it>M. tuberculosis </it>H37Rv and the clinical strain <it>M. tuberculosis </it>CDC1551 are available, the clinical isolates from India have not been studied extensively at the genome level. This study was carried out in order to have a better understanding of isolates from Kerala, a state in southern India.</p> <p>Results</p> <p>A PCR based strategy was followed making use of the deletion region primers to understand the genome level differences between the type strain H37Rv and the clinical isolates of <it>M. tuberculosis </it>from Kerala. PCR analysis of patient isolates using RD1 region primers revealed the amplification of a 386 bp region, in addition to the expected 652 bp amplicon. Southern hybridization of genomic DNA with the 386 bp amplicon confirmed the presence of this new region in a majority of the patient isolates from Kerala. Sequence comparison of this amplicon showed close homology with the <it>moa</it>A3 gene of <it>M. bovis</it>. In <it>M. bovis </it>this gene is present in the RvD5 region, an IS<it>6110 </it>mediated deletion that is absent in <it>M. tuberculosis </it>H37Rv.</p> <p>Conclusion</p> <p>This study demonstrates the presence of <it>moa</it>A3 gene, that is absent in <it>M. tuberculosis </it>H37Rv and H37Ra, in a large number of local isolates. Whether the <it>moa</it>A3 gene provides any specific advantage to the field isolates of the pathogen is unclear. Field strains from Kerala have fewer IS<it>6110 </it>sequences and therefore are likely to have fewer IS<it>6110 </it>dependent rearrangements. But as deletions and insertions account for much of the genomic diversity of <it>M. tuberculosis</it>, the mechanisms of formation of sequence polymorphisms in the local isolates should be further examined. These results suggest that studies should focus on strains from endemic areas to understand the complexities of this pathogen.</p
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