The Emerging Crisis of Antibiotic Resistance in South African Waterways

Antibiotic resistance, often abbreviated as antimicrobial resistance or AMR, occurs when bacteria evolve mechanisms to withstand drugs designed to kill them, rendering standard treatments ineffective. In South Africa, this global health challenge is intensifying through environmental pathways, particularly wastewater treatment plants (WWTPs). These facilities process sewage from households, hospitals, industries, and abattoirs, but recent university-led research reveals they may inadvertently release antimicrobial resistance genes (ARGs) into rivers, creating ecological hotspots for superbugs.

South Africa's unique context amplifies the risk. With aging infrastructure—334 out of 850 WWTPs rated critical by the Green Drop Report—and high antibiotic use in healthcare and agriculture, untreated or partially treated effluents carry resistant bacteria and free-floating genetic material into rivers. These waterways supply drinking water, irrigation, and recreation, potentially cycling resistance back to humans via contaminated food, water, or direct contact.

Stellenbosch University's Groundbreaking Discovery in Tshwane

Researchers at Stellenbosch University (SU), under the DSI/NRF South African Research Chair Initiative (SARChI) in African Microbiome Innovation, have pioneered a study examining ARGs in the urban wastewater-river continuum of Tshwane, South Africa's administrative capital. Led by medical microbiologist Dr. John Paul Makumbi and chaired by Prof. Thulani Makhalanyane, the team sampled nine WWTPs from February to May 2023, analyzing influents, effluents, and upstream/downstream river sites using advanced shotgun metagenomics.

Their work, published in Cell Reports on March 31, 2026, titled "Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum," uncovers how WWTPs act as "superspreaders." Even as bacteria are killed during treatment, extracellular DNA (exDNA)—genetic fragments released from lysed cells—persists, carrying ARGs that can be taken up by other microbes via horizontal gene transfer.Read the full study here.

Mechanisms of ARG Persistence Through Wastewater Treatment

Conventional WWTPs in South Africa primarily use activated sludge processes (ASP), sometimes combined with biofilters. The SU study compared single-stage ASP-only plants with multi-stage ASP-biofilter systems. Surprisingly, no significant ARG reduction occurred from influent to effluent across all sites (Kruskal-Wallis test, p > 0.05). In six of nine plants, effluent ARG counts exceeded influents.

High-risk ARGs conferring resistance to last-resort antibiotics—like carbapenems (blaTHIN-B, blaJOHN, blaCAU), cephalosporins (blaMOX), beta-lactams (blaAER, blaSCO, blaOXA), aminoglycosides (aph, aad), and quinolones—dominated. About 25% (140 of 561 ARGs) were mobile, linked to plasmids (90%) and phages, facilitating spread.

• Single-stage ASP: ARG accumulation for aminoglycosides, beta-lactams, carbapenems, sulfonamides.
• Multi-stage ASP-biofilter: Better removal for some classes (e.g., MLSb, rifamycins), but high-risk genes persisted.

Downstream rivers showed elevated ARGs compared to upstream sites, indicating cumulative WWTP inputs reshape river microbiomes.

Bacterial Groups Driving the Resistance Threat

Metagenomic analysis pinned ARGs primarily to two phyla: Pseudomonadota (formerly Proteobacteria) and Bacteroidota. These opportunistic pathogens, like Pseudomonas aeruginosa and Escherichia coli, thrive in wastewater and exhibit multidrug resistance. Metagenome-assembled genomes (MAGs) from Emticicia (Bacteroidota) highlighted multiple drug resistance potential.

Upstream rivers already harbored 84 ARGs, suggesting diffuse pollution from agriculture, informal settlements, and non-point sources. However, effluents amplified specific high-risk profiles, turning rivers into dissemination vectors.

Broader South African Research Landscape

SU's findings align with a 2026 narrative review by University of Venda researchers, analyzing 24 studies from 2009–2024. It documents rising resistance in WHO critical priority enteric bacteria: E. coli (tetracycline 43–100%, ampicillin 67–94%), Enterococcus spp. (vancomycin 62–93.6%), Klebsiella pneumoniae (carbapenems 51–69%).Access the review.

In the Eastern Cape, Walter Sisulu University studies detected high antibiotic residues and ARGs (e.g., sul1, tetA) in WWTP effluents and receiving rivers, with incomplete removal. North-West University reported ARV and antibiotic persistence downstream. These university efforts underscore AMR's One Health dimensions—linking human, animal, and environmental health.

Health and Environmental Impacts

AMR claims 9,500 direct deaths annually in South Africa, with 39,000 associated indirectly, amid HIV/TB burdens. Globally, 4.95 million deaths yearly. Environmentally, ARG-enriched rivers contaminate irrigation water, fostering resistant crops and livestock. Recreational exposure risks infections; reclaimed water for industry heightens occupational hazards.

Rivers like those in Tshwane support millions, yet act as reservoirs where exDNA enables gene hopping, accelerating evolution toward untreatable superbugs.

Infrastructure Challenges in South Africa

Many WWTPs predate modern AMR threats, lacking tertiary treatments like UV or ozonation. Overflows during rains bypass processes; industrial/hospital inputs overwhelm capacities. The 2022 Green Drop Report flags systemic failures, with population growth straining systems in urban hubs like Tshwane and Eastern Cape.

Innovative Solutions from Academic Research

South African universities propose targeted upgrades:

• Pretreat high-risk effluents (hospitals, abattoirs) before WWTP entry.
• Adopt multi-stage treatments: UV disinfection, advanced oxidation, membrane bioreactors for exDNA/ARG removal.
• Wastewater-based surveillance using metagenomics for early detection.
• Antibiotic stewardship and public education to curb usage.

The Pivotal Role of Universities in AMR Combat

Institutions like SU, University of Pretoria, Walter Sisulu, and University of Venda lead with SARChI chairs, Water Research Commission grants, and international collaborations (e.g., QUT Australia). Their multi-omics expertise fills gaps in Africa's resistome mapping, informing national strategies.

Emerging researchers like Dr. Makumbi exemplify career paths in microbiome innovation, blending microbiology, bioinformatics, and environmental science.SU news release.

Photo by Dieter Wolf on Unsplash

Future Outlook: Toward Resilient Water Systems

By 2050, AMR could cause 10 million global deaths yearly without action. South Africa's universities advocate One Health frameworks, investing in biosensors, predictive modeling, and policy. Upgrading WWTPs could stem ARG flow, safeguarding rivers, public health, and ecosystems for generations.