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Background  Aminoglycosides such as amikacin and kanamycin are effective injectable second-line drugs for treatment of multidrug-resistant tuberculosis. Molecular mechanisms underlying aminoglycoside resistance are not well understood. We have previously identified the amikacin- and kanamycin-resistant  M. tuberculosis  MT433 clinical strain, of which all known mutations related to resistance have not been found. Drug efflux pump is one of reported resistance mechanisms that might play a role in aminoglycoside resistance.    Methods  The expression levels of sixteen putative efflux pump genes, including  eis  and one regulator gene,  whiB7 , of MT433 in the presence of kanamycin were determined using the reverse transcription-quantitative PCR method. The effects of upregulated genes on amikacin and kanamycin resistance were investigated by overexpression in  M. tuberculosis  H37Ra strain.    Results  Upon kanamycin exposure, other than  whiB7  and  eis  that were found extremely overexpressed, two drug efflux pump genes, namely Rv1877 and Rv2846c, showed specifically high-level of expression in  M. tuberculosis  MT433 strain. However, direct effect of overexpressed Rv1877 and Rv2846c on amikacin and kanamycin resistance could not be demonstrated in  M. tuberculosis  H37Ra overexpressed strain.    Conclusions  Our finding demonstrated that overexpression of  eis  could occur without any mutations in the promoter region and be detectable in clinical isolate. This might be a consequence of overexpressed  whiB7 , resulting in amikacin and kanamycin resistance in  M. tuberculosis  MT433 strain.    Electronic supplementary material  The online version of this article (10.1186/s12941-018-0285-6) contains supplementary material, which is available to authorized users.

Overexpression of eis without a mutation in promoter region of amikacin- and kanamycin-resistant Mycobacterium tuberculosis clinical strain