In the heart of South Africa’s bustling urban landscape, a silent but potent threat is seeping through its water systems, carried not by whole bacteria, but by fragments of genetic material that survive traditional wastewater treatments. Recent groundbreaking research led by Stellenbosch University reveals that extracellular DNA (exDNA) — genetic remnants released from bacteria killed during wastewater treatment — may play a pivotal role in harboring and spreading antimicrobial resistance genes. These findings challenge long-held assumptions about the effectiveness of wastewater treatment plants (WWTPs) and raise urgent concerns about the persistence and transmission of antibiotic resistance in the environment.
Antimicrobial resistance (AMR) is a looming global health crisis, threatening to render current antibiotics useless against common infections. AMR arises when bacteria evolve mechanisms to withstand antimicrobial drugs, complicating treatments and amplifying the risk of fatal infections. Alarmingly, projections indicate that if unchecked, AMR could claim up to 10 million lives annually by 2050. While much focus has been placed on clinical settings, the environmental reservoirs of AMR, especially in urban water systems, remain critically understudied.
The research team, anchored at Stellenbosch University under the leadership of Dr. John Paul Makumbi, conducted an extensive microbiome analysis along an urban wastewater-river continuum in Tshwane, South Africa. Their investigation specifically targeted how AMR genes persist not through living bacteria but within extracellular DNA expelled during bacterial cell death. The study highlights how WWTPs, originally designed to detoxify harmful chemicals and eliminate live bacteria, are not sufficiently equipped to degrade or remove this genetic material.
This revelation is crucial because conventional wastewater treatment methods overlook exDNA as a vector for resistance gene transmission. The treated effluent, even after passing through multiple purification stages, still carries exDNA harboring high-risk resistance genes. Within this genetic soup reside fragments from two major bacterial phyla known for their notorious multi-drug resistant strains: Pseudomonadota and Bacteroidota. These groups’ resistance profiles have long been associated with clinical and environmental challenges, indicating that their genetic material’s survival in exDNA form poses an overlooked epidemic risk.
Dr. Makumbi explains that although the physical bacteria may be eradicated by WWTP processes, the exDNA carrying resistance determinants can persist in the discharged water, potentially transferring these genes horizontally to other bacteria in the environment. “This extracellular DNA represents a genetic reservoir that can perpetuate the cycle of antibiotic resistance, acting as an ecological superspreader within aquatic ecosystems,” he notes. This mechanism challenges traditional perspectives on microbial survival and resistance spread in municipal water systems.
The implications are profound for urban ecosystem health and public safety. Wastewater treatment plants, often perceived as barriers against microbial threats, could instead act as hotbeds for the enrichment and spread of antimicrobial resistance via exDNA. This poses a risk not only to aquatic life but also to human populations reliant on these water sources for consumption, agriculture, or recreation. The ability of exDNA to facilitate gene transfer across bacterial species compounds the complexity of managing AMR in the environment.
Currently, some WWTPs worldwide, including several in South Africa, are exploring advanced technological upgrades such as ultraviolet (UV) treatment to target AMR genes more effectively. However, these interventions are unevenly implemented and far from universal. Dr. Makumbi advocates for accelerated investment in upgrading the infrastructure to integrate such advanced treatment modalities. “Protecting our waterways means pre-treating effluent from high-risk origin sources like abattoirs, hospitals, and industrial facilities before it reaches the main wastewater system,” he stresses.
Moreover, the research underscores the intertwined challenges of water security and antimicrobial resistance in Africa’s urban centers. According to Professor Thulani Makhlanyane, who holds the DSTI-NRF research chair in African Microbiome Innovation, the continent faces compounded risks due to aging water infrastructure, insufficient management, and the slow integration of scientific findings into policy frameworks. “Future conflicts will increasingly hinge on water security and microbial resilience,” Makhlanyane warns, highlighting the need for informed, science-driven governance.
The study reflects a broader call to action for governments, industry, and scientific communities to prioritize interdisciplinary research and investment in water quality management. It encourages redefining wastewater treatment goals to include the mitigation of genetic-level contamination and antimicrobial resistance gene proliferation. The water environment, traditionally seen as a passive receptacle for waste, must be re-envisioned as an active battleground for controlling AMR’s dissemination.
Published in the prestigious journal Cell Reports, this research marks a significant step forward in understanding the genetic dynamics of AMR beyond living organisms. By exposing the invisible threat posed by exDNA, the study highlights a critical blind spot in environmental microbiology and public health. The pathways through which antibiotic resistance genes traverse natural and engineered ecosystems require urgent remedial innovation and public awareness to avert a looming post-antibiotic era.
As urban populations grow and the demand on water resources intensifies, integrating scientific insights such as those provided by the Stellenbosch University team into environmental policies becomes indispensable. Protecting freshwater systems from becoming reservoirs and conduits of antimicrobial resistance is not only an ecological imperative but also a cornerstone of safeguarding human health globally. This emerging research calls for a transformative shift in how we conceptualize and manage microbial risk in the environment.
In conclusion, the persistence of high-risk antimicrobial resistance genes within extracellular DNA along urban wastewater and river systems presents a novel transmission risk that conventional treatment systems inadequately address. The findings underscore the necessity for enhanced wastewater treatment technologies, integrated water management policies, and robust surveillance frameworks to curtail the environmental dimension of antimicrobial resistance. Addressing this challenge head-on offers a tangible path towards preserving the efficacy of antibiotics and maintaining water security in an increasingly interconnected world.
Subject of Research: Cells
Article Title: Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum
News Publication Date: 30-Mar-2026
Web References: https://doi.org/10.1016/j.celrep.2026.117128
References: Makumbi, J.P., et al. (2026). Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum. Cell Reports. https://doi.org/10.1016/j.celrep.2026.117128
Image Credits: JP Makumbi
Keywords: antimicrobial resistance, extracellular DNA, wastewater treatment plants, environmental microbiology, Pseudomonadota, Bacteroidota, water security, gene transfer, urban wastewater, antibiotic resistance genes
