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Background  Genome sequencing and genetic polymorphism analysis of clinical isolates of  M. tuberculosis  is carried out to gain further insight into molecular pathogenesis and host-pathogen interaction. Therefore the functional evaluation of the effect of single nucleotide variation (SNV) is essential. At the same time, the identification of invariant sequences unique to  M. tuberculosis  contributes to infection detection by sensitive methods. In the present study, genome analysis is accompanied by evaluation of the functional implication of the SNVs in a MDR clinical isolate VPCI591.    Result  By sequencing and comparative analysis of VPCI591 genome with 1553 global clinical isolates of  M. tuberculosis  (GMTV and tbVar databases), we identified 141 unique strain specific SNVs. A novel intergenic variation in VPCI591 in the putative promoter/regulatory region mapping between  embC  ( Rv3793 ) and  embA  ( Rv3794 ) genes was found to enhance the expression of  embAB , which correlates with the high resistance of the VPCI591 to ethambutol. Similarly, the unique combination of three genic SNVs in RNA polymerase β gene ( rpoB ) in VPCI591 was evaluated for its effect on rifampicin resistance through molecular docking analysis.  The comparative genomics also showed that along with variations, there are genes that remain invariant. 173 such genes were identified in our analysis.    Conclusion  The genetic variation in  M. tuberculosis  clinical isolate VPCI591 is found in almost all functional classes of genes. We have shown that SNV in  rpoB  gene mapping outside the drug binding site along with two SNVs in the binding site can contribute to quantitative change in MIC for rifampicin. Our results show the collective effect of SNVs on the structure of the protein, impacting the interaction between the target protein and the drug molecule in  rpoB  as an example. The study shows that intergenic variations bring about quantitative changes in transcription in  embAB  and in turn can lead to drug resistance.

bmc microbiology

Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis