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

Keira Tucker, Leonardos Mageiros, Alno Carstens, Ludwig Bröcker, Edward Archer, Katrin Smith, Evangelos Mourkas, Ben Pascoe, Daan Nel, Guillaume Meric, Samuel K. Sheppard, Barbara Kasprzyk-hordern, Marelize Botes, Edward J. Feil, Gideon Wolfaardt, Blaire Steven (Editor)

Research output: Contribution to journalArticlepeer-review

3 Citations (SciVal)


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.
Original languageEnglish
Article numberE02473-22
JournalMicrobiology Spectrum
Issue number5
Early online date29 Aug 2022
Publication statusPublished - 26 Oct 2022

Bibliographical note

Funding Information:
We declare no competing interests. This work is based on the research supported in part by the National Research Foundation of South Africa (Grant numbers: 118160 and 130527) and the Global Challenges Research Fund (EP/P028403/1). Conceptualization, K.T., L.M., E.J.F., M.B., G.W.; design of experimentation, sampling, and wet lab data acquisition, K.T., A.C., L.B., E.A. K.S., L.M., B.P.; data analysis K.T., L.M., E.M., D.N.; manuscript writing, K.T., L.M.; funding acquisition, B.K.H.; manuscript editing, M.B., E.J.F., G.W., B.K.-H.

Funding Information:
Thank you to the Stellenbosch Wastewater treatment plant and Cape Nature for permitting sampling. The support of the Global Challenges Research Fund and Engineering and Physical Sciences Research Council (EP/P028403/1) is greatly appreciated.



  • antimicrobial resistance
  • metagenomics
  • one health
  • surface water
  • wastewater
  • wastewater treatment

ASJC Scopus subject areas

  • Physiology
  • Ecology
  • Immunology and Microbiology(all)
  • Genetics
  • Microbiology (medical)
  • Cell Biology
  • Infectious Diseases


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