Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity

With increasing emergence of antimicrobial resistant bacteria (ARB) and the risk this poses to public health, there are growing concerns regarding water pollution contributing to the spread of antimicrobial resistance (AMR) through inadequate amenities and the rapid rate of urbanization. In this study, the impact of different anthropogenic factors on the prevalence of AMR in the urban water cycle in Stellenbosch, South Africa (SA) was examined. Carbapenem, colistin, gentamicin and sulfamethoxazole resistant Gram-negative bacteria were recovered by selectively culturing aqueous, biofilm and sediment samples from sites impacted to varying degrees by informal settlements, residential, industrial, and agricultural activities, as well as a municipal wastewater treatment works (WWTW). A metagenomic approach determined community profiles and dominant AMR genes at various sites, while carbapenem resistant colonies were characterized using whole genome sequencing (WGS). Isolates recovered from agricultural sites exhibited relatively high levels of resistance to carbapenems and colistin, whereas sites impacted by domestic run-off had a higher prevalence of resistance to gentamicin and sulfamethoxazole, corresponding to usage data in SA. Similar microbial taxa were identified in raw sewage, sites downstream of informal settlements, and industrial areas that have limited waste removal infrastructure while WWTW were seen to reduce the prevalence of ARB in treated wastewater when operating efficiently. The results indicate the multiple complex drivers underpinning environmental dissemination of AMR and suggest that WWTW assist in removing AMR from the environment, reinforcing the necessity of adequate waste removal infrastructure and antibiotic stewardship measures to mitigate AMR transmission.