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Background  Molecular analysis of carbapenem-resistant genes in  Acinetobacter baumannii , an emerging pathogen, is less commonly reported from Nepal. In this study we determined the antibiotic susceptibility profile and genetic mechanism of carbapenem resistance in clinical isolates of  A. baumannii.Methods    A. baumannii  were isolated from various clinical specimens and identified based on Gram staining, biochemical tests, and PCR amplification of organism specific 16S rRNA and  bla   OXA-51  genes. The antibiotic susceptibility testing was performed using disc diffusion and E-test method. Multiplex PCR assays were used to detect the following β-lactamase genes: four class D carbapenem hydrolyzing oxacillinases ( bla   OXA-51 ,  bla   OXA-23 ,  bla   OXA-24  and  bla   OXA-58 ). Uniplex PCRs were used to detect three class B metallo-β-lactamases genes ( bla   IMP ,  bla   VIM  and  bla   NDM-1 ), class C cephalosporin resistance genes ( bla   ADC ), aminoglycoside resistance gene ( aphA6 ), and IS Aba1  of all isolates. Insertion sequence IS Aba125  among NDM-1 positive strains was detected. Clonal relatedness of all isolates were analyzed using repetitive sequence-based PCR (rep-PCR).    Results  Of total 44 analyzed isolates, 97.7% ( n  = 43) were carbapenem-resistant  A. baumannii  (CR-AB) and 97.7% ( n  = 43) were multidrug resistant  A. baumannii  (MDR-AB). One isolate was detected to be extremely drug resistant  A. baumannii  (XDR-AB). All the isolates were fully susceptible to colistin (MICs < 2 μg/ml). The  bla   OXA-23  gene was detected in all isolates, while  bla   NDM-1  was detected in 6 isolates (13.6%). Insertion sequence, IS Aba1  was detected in all of  bla   OXA-23  positive isolates. IS Aba125  was detected in all  bla   NDM-1  positive strains. The  bla   ADC  and  aphA6  genes were detected in 90.1 and 40.1%, respectively. The rep-PCR of all isolates represented 7 different genotypes.    Conclusion  We found high prevalence of CR-AB and MDR-AB with  bla   OXA-23  gene in a tertiary care hospital in Nepal. Systemic network surveillance should be established for monitoring and controlling the spread of these resistant strains.    Electronic supplementary material  The online version of this article (doi:10.1186/s13756-017-0180-5) contains supplementary material, which is available to authorized users.

Co-existence of bla OXA-23 and bla NDM-1 genes of Acinetobacter baumannii isolated from Nepal: antimicrobial resistance and clinical significance