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Background  Carbapenem-resistant  Acinetobacter baumannii  has recently been defined by the World Health Organization as a critical pathogen. The aim of this study was to compare clonal diversity and carbapenemase-encoding genes of  A. baumannii  isolates collected from colonized or infected patients and hospital environment in two intensive care units (ICUs) in Morocco.    Methods  The patient and environmental sampling was carried out in the medical and surgical ICUs of Mohammed V Military teaching hospital from March to August 2015. All  A. baumannii  isolates recovered from clinical and environmental samples, were identified using routine microbiological techniques and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using disc diffusion method. The carbapenemase-encoding genes were screened for by PCR. Clonal relatedness was analyzed by digestion of the DNA with low frequency restriction enzymes and pulsed field gel electrophoresis (PFGE) and the multi locus sequence typing (MLST) was performed on two selected isolates from two major pulsotypes.    Results  A total of 83 multidrug-resistant  A. baumannii  isolates were collected: 47 clinical isolates and 36 environmental isolates. All isolates were positive for the  bla    OXA51-like   and  bla    OXA23-like   genes. The coexistence of  bla    NDM-1    /bla    OXA-23-like   and  bla    OXA 24-like    /bla    OXA-23-like   were detected in 27 (32.5%) and 2 (2.4%) of  A. baumannii  isolates, respectively. The environmental samples and the fecally-colonized patients were significantly identified ( p  &lt; 0.05) as the most common sites of isolation of NDM-1-harboring isolates. PFGE grouped all isolates into 9 distinct clusters with two major groups (0007 and 0008) containing up to 59% of the isolates. The pulsotype 0008 corresponds to sequence type (ST) 195 while pulsotype 0007 corresponds to ST 1089.The genetic similarity between the clinical and environmental isolates was observed in 80/83 = 96.4% of all isolates, belonging to 7 pulsotypes.    Conclusion  This study shows that the clonal spread of environmental  A. baumannii  isolates is related to that of clinical isolates recovered from colonized or infected patients, being both associated with a high prevalence of the  bla    OXA23-like   and  bla    NDM-1  genes. These findings emphasize the need for prioritizing the bio-cleaning of the hospital environment to control and prevent the dissemination of  A. baumannii  clonal lineages.    Electronic supplementary material  The online version of this article (10.1186/s13756-017-0262-4) contains supplementary material, which is available to authorized users.

antimicrobial resistance and infection control

Clonal diversity and detection of carbapenem resistance encoding genes among multidrug-resistant Acinetobacter baumannii isolates recovered from patients and environment in two intensive care units in a Moroccan hospital