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Background  Multidrug resistant  Pseudomonas aeruginosa  and  Acinetobacter baumannii  are common causes of health care associated infections worldwide. Carbapenems are effective against infections caused by multidrug resistant Gram-negative bacteria including  Pseudomonas  and  Acinetobacter  species. However, their use is threatened by the emergence of carbapenemase-producing strains. The aim of this study was to determine the prevalence of carbapenem-resistant  P. aeruginosa  and  A. baumannii  at Mulago Hospital in Kampala Uganda, and to establish whether the hospital environment harbors carbapenem-resistant Gram-negative rods.    Results  Between February 2007 and September 2009, a total of 869 clinical specimens were processed for culture and sensitivity testing yielding 42 (5 %)  P. aeruginosa  and 29 (3 %)  A. baumannii  isolates, of which 24 % (10/42)  P. aeruginosa  and 31 % (9/29)  A. baumannii  were carbapenem-resistant. Additionally, 80 samples from the hospital environment were randomly collected and similarly processed yielding 58 % (46/80)  P. aeruginosa  and 14 % (11/80)  A. baumannii , of which 33 % (15/46)  P. aeruginosa  and 55 % (6/11)  A. baumannii  were carbapenem-resistant. The total number of isolates studied was 128. Carbapenemase genes detected were  bla  IMP -like (36 %, 9/25),  bla  VIM -like (32 %, 8/25),  bla  SPM -like (16 %, 4/25);  bla  NDM-1 -like (4 %, 1/25) in carbapenem-resistant  P. aeruginosa , and  bla  OXA-23 -like (60 %, 9/15),  bla  OXA-24 -like (7 %, 1/15),  bla  OXA-58 -like (13 %, 2/15), and  bla  VIM -like (13 %, 2/15) in carbapenem-resistant  A. baumannii . Furthermore, class 1 integrons were detected in 38 % (48/128) of  P. aeruginosa  and  Acinetobacter , 37 % (26/71) of which were in clinical isolates and 39 % (22/57) in environment isolates. Gene cassettes were found in 25 % (12/48) of integron-positive isolates. These were aminoglycoside adenylyltransferase  ant(4′) - IIb  (3 isolates); trimethoprim-resistant dihydrofolate reductase  dfrA  (2 isolates); adenyltransferase  aadAB  (3 isolates);  QacE  delta1 multidrug exporter (2 isolates); quinolone resistance pentapeptide repeat protein  qnr  (1 isolate); and metallo-β-lactamase genes  bla  VIM-4 -like,  bla  IMP-19 -like, and  bla  IMP-26 -like (1 isolate each). Gene cassettes were missing in 75 % (36/48) of the integron-positive isolates.    Conclusions  The prevalence of carbapenem-resistant  P. aeruginosa  and  Acinetobacter  among hospitalized patients at Mulago Hospital is low compared to rates from South-East Asia. However, it is high among isolates and in the environment, which is of concern given that the hospital environment is a potential source of infection for hospitalized patients and health care workers.    Electronic supplementary material  The online version of this article (doi:10.1186/s40064-016-2986-7) contains supplementary material, which is available to authorized users.

Carbapenem resistant Pseudomonas aeruginosa and Acinetobacter baumannii at Mulago Hospital in Kampala, Uganda (2007–2009)