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Conclusion In this study, genetic analysis showed that only one-fourth XDR-TB isolates had a mutation in the atpE gene; there were no other mutations found in the Rv0678 gene. To the best of our knowledge, this novel mutation (L-49-P) in atpE gene is being reported for the first time in northern India.Background Mycobacterium leprae is a noncultivable mycobacteria, and diagnosis of the disease is based on its clinical and histopathological characteristics and finding the bacteria in skin scrapings and in biopsies taken from the patient