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Background  Colistin is regarded as a last-resort antimicrobial against multi-drug resistant Gram-negative bacteria (GNB), therefore the dissemination of colistin resistance in the environment is of great concern. Horizontal transfer of mobile colistin resistance ( mcr ) genes to potential pathogens poses a serious problem. This study aimed to describe the presence of colistin resistant GNB and  mcr  genes in river and storm water in regions of the Western Cape.    Methods  Water samples were collected from three rivers during May 2019 and January 2020 and two storm water samples were collected in November 2019. Colistin resistant GNB were cultured on MacConkey agar containing colistin and identified by MALDI-TOF. Colistin resistance was confirmed using broth microdilution (BMD).  mcr-1-5  genes were detected by PCR performed directly on the water samples and on the colistin resistant isolates.  mcr  functionality was assessed by BMD after cloning the  mcr  genes into pET-48b(+) and expression in SHuffle T7  E. coli .    Results   mcr-5.1  and various  mcr-3  gene variants were detected in the Plankenburg-, Eerste- and Berg rivers and in storm water from Muizenberg, and only  mcr-5.1  was detected in storm water from Fish Hoek. Colistin resistant GNB were isolated from all of the water sources.  Aeromonas  spp. were the most common colistin resistant organisms detected in the water sources; 25% (6/24) of colistin resistant  Aeromonas  spp. isolated from the Berg river contained novel  mcr-3  variants;  mcr-3.33  (n = 1),  mcr-3.34  (n = 1)  mcr-3.35  (n = 1)  mcr-3.36  (n = 2) and  mcr-3.37  (n = 1), which were confirmed to confer colistin resistance.    Conclusions  The  mcr-5.1  and  mcr-3  colistin resistance gene variants were present in widely dispersed water sources in regions of the Western Cape. The  mcr  genes were only detected in water sampled downstream of and alongside communities, suggesting that their presence is driven by human influence/contamination. This is the first documentation of  mcr-3  and  mcr-5  gene variants in any setting in South Africa. Spill-over of these genes to communities could result in horizontal gene transfer to pathogenic bacteria, exacerbating the challenge of controlling multidrug resistant GNB infections.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13756-021-00963-2.

Characterisation of mobile colistin resistance genes (mcr-3 and mcr-5) in river and storm water in regions of the Western Cape of South Africa