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<p>Abstract</p> <p>Background</p> <p>Comparative genomic analysis of <it>M. tuberculosis </it>H37Rv and <it>M. bovis </it>BCG have shown that 16 RDs (Regions of Differences) are deleted in BCG and have shown six deletion regions in <it>M. tuberculosis </it>H37Rv. RD1, is present in <it>M. tuberculosis </it>but is absent in all <it>M. bovis </it>BCG sub-strains. A study from Kerala, a south-western coastal state of India aimed to find out differences in RD1 region showed for the first time the presence of moaA3 gene in majority of their clinical isolates, that was absent in type strain H37Rv. We attempted to find out such polymorphism between type strains and the clinical isolates within RD1, targeting moaA3 gene among the clinical isolates of Tamil Nadu & Pondicherry, south-eastern coastal states of India</p> <p>Methods</p> <p>One hundred and sixteen clinical isolates of <it>M. tuberculosis </it>were included in the study. PCR using RD1DLa and RD1DRa primers was carried out to amplify a 652 bp fragment, encoding for <it>cfp</it>10 and <it>esat </it>6 proteins of RD1. A second PCR using primers designed from the surrounding regions of <it>moa</it>A3 gene was done to confirm the presence of the full Open Reading Frame (ORF) in clinical isolates.</p> <p>Results</p> <p>In <it>M. tuberculosis </it>H37Rv the expected 652 bp band was present. In BCG it was absent as expected, but a 386 bp fragment was amplified. Around 12/116 (10.3%) of our clinical isolates showed both 652 and 386 bp fragments. The additional 386 bp amplicon is a part of the <it>moaA3 </it>gene which codes for molybdopterin cofactor protein A in <it>M. bovis</it>. The second PCR amplified the flanking sequence of <it>moaA3 </it>and yielded the expected amplicon of 1254 bp in all those 10.3% of clinical isolates which had the 386 bp fragment. However the earlier study carried out in Kerala, reported the presence of <it>moaA3 </it>gene in majority (97%) of their clinical isolates.</p> <p>Conclusion</p> <p>This finding showed that there was regional variation presenting polymorphism in <it>moA3 </it>gene, among the strains of <it>M. tuberculosis </it>and further strengthens the speculation of genetic differences among the strains of Kerala and Tamil Nadu & Pondicherry, the South Indian states</p>