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Gram-negative multidrug-resistant organisms (GN-MDRO) producing β-lactamases (ESBL, plasmid-mediated AmpC β-lactamases and carbapenemases) are increasingly reported throughout Asia. The aim of this surveillance study was to determine the rate of bacterial colonization in patients from two hospitals in the Mongolian capital Ulaanbaatar. Rectal swabs were obtained from patients referred to the National Traumatology and Orthopaedics Research Centre (NTORC) or the Burn Treatment Centre (BTC) between July and September 2014, on admission and again after 14 days. Bacteria growing on selective chromogenic media (CHROMagar ESBL/KPC) were identified by MALDI-ToF MS. We performed susceptibility testing by disk diffusion and PCR (blaIMP-1, blaVIM, blaGES, blaNDM, blaKPC, blaOXA-48, blaGIM-1, blaOXA-23, blaOXA-24/40, blaOXA-51, blaOXA-58, blaOXA-143, blaOXA-235, blaCTX-M, blaSHV blaTEM and plasmid-mediated blaAmpC). Carbapenemase-producing isolates were additionally genotyped by PFGE and MLST. During the study period 985 patients in the NTORC and 65 patients in the BTC were screened on admission. The prevalence of GN-MDRO-carriage was 42.4% and 69.2% respectively (p<0.001). Due to the different medical specialities the two study populations differed significantly in age (p<0.029) and gender (p<0.001) with younger and more female patients in the burn centre (BTC). We did not observe a significant difference in colonization rate in the respective age groups in the total study population. In both centres most carriers were colonized with CTX-M-producing E. coli, followed by CTX-M-producing K. pneumoniae and CTX-M-producing E. cloacae. 158 patients from the NTORC were re-screened after 14 days of whom 99 had acquired a new GN-MDRO (p<0.001). Carbapenemases were detected in both centres in four OXA-58-producing A. baumannii isolates (ST642) and six VIM-2-producing P. aeruginosa isolates (ST235). This study shows a high overall prevalence of GN-MDRO in the study population and highlights the importance of routine surveillance, appropriate infection control practice and antibiotic prescribing policies to prevent further spread especially of carbapenemases.