An ecological approach to risk characterisation of antimicrobial resistance from South African urban wastewater and freshwater microbiomes

Abstract

Antimicrobial resistance (AMR) is routinely called ‘the silent pandemic’ despite the substantial impact on public health. Natural and engineered environmental systems such as rivers and wastewater treatment plants (WWTPs), may be AMR reservoirs and hotspots. However, we lack comprehensive insights regarding the role of these ecosystems in environmental AMR persistence and dissemination. There is a substantial lack of data on the key ecological parameters that influence AMR dynamics as well as the primary proxies necessary for evaluating dissemination risks. Notably, the potential role of extracellular DNA (exDNA), in facilitating the persistence of antimicrobial resistance genes (ARGs), remains underexplored.

This study combined metagenomics to identify antimicrobial resistant bacteria (ARB) and ARGs, with chemical analyses, including liquid chromatography-mass spectrometry (LC-MS) and in-situ measurements, to assess resistome persistence and transition in nine urban WWTPs and associated rivers in Tshwane, South Africa. The findings showed that WWTPs are ineffective at removing high-risk ARGs, including beta-lactamase (bla), aminoglycoside (aac, aad, ant, aph) and mobile colistin resistance (mcr) genes, which are associated with resistance to critically important antibiotics, with effluents showing higher ARG abundance (p ≤ 0.05) than influents. This resulted in the dissemination of ARGs and ARB into rivers, leading to higher ARG occurrences at downstream sites compared to upstream. Environmental compartmentalisation between the water column and sediment microenvironments influenced AMR persistence and dissemination in the receiving rivers. River pelagic zones appear to be crucial for the spread of pathogenic ARB, while sediments were major reservoirs for ARGs. Physicochemical factors, including temperature, pH, nutrients and heavy metal contaminants, substantially influenced ARG distribution. The findings support the assertion that physicochemical factors may be valid proxies for AMR surveillance and risk assessment. Analysis of exDNA demonstrated its underestimated role in shaping AMR patterns in these aquatic systems. To our knowledge, this is the first study to investigate exDNA-associated AMR in an African wastewater and freshwater system. exDNA predominantly carried several high-risk ARGs. These data suggest potential increased risk of AMR persistence in effluents and rivers, with 66% of the WWTPs showing higher ARG counts in effluents compared with influents. The exDNA resistome also suggests high horizontal gene transfer (HGT) potential, driven by mobile ARGs on plasmids and bacteriophages. Notably, WWTPs using combined activated sludge process (ASP) and biofilter (ASP-biofilter) treatment methods showed reduced ARG diversity in the effluents compared to those using ASP-only treatment. However, the differences in ARG abundance between influents and effluents were not statistically significant (p = 0.05). This finding suggests that WWTPs employing additional treatment stages beyond conventional ASP may help reduce AMR dissemination risks. This study highlights the potential benefits of incorporating ecosystem-based approaches into AMR control practices. Specifically, improving ARG removal efficacy at WWTPs is as crucial as reducing antimicrobial-resistant bacterial load. This may be achieved through the implementation of additional barriers such as biofiltration. More broadly, the findings from this thesis emphasise the importance of integrated frameworks to monitor how environmental stressors and anthropogenic influence shape microbial evolution, particularly in pathogenic species that pose a public health risk.