Health action needed as environmental reservoirs fuel drug-resistant infections

Environmental antimicrobial resistance is turning rivers, soils and even the air into hidden highways for “superbugs,” according to a new review that calls for urgent, coordinated action for human, animal and environmental health. The authors argue that protecting people from drug-resistant infections now depends as much on sewage plants and farms as it does on hospitals.

A growing ‘superbug’ environmental crisis.

Antimicrobial resistance (AMR) occurs when bacteria and other microbes develop the ability to survive drugs that once killed them, making common infections more difficult or impossible to treat. The World Health Organization already ranks AMR as one of the most serious global health threats of this century, with some estimates warning of tens of millions of deaths and huge economic losses if action fails.

The new study shows that the environment is not just a passive backdrop. Rivers, lakes, soils, oceans and even the air can carry resistance genes and resistant bacteria that move between wildlife, animals and people, helping to create a truly global AMR network.​

Key sources and hidden reservoirs

The review highlights several important environmental hotspots where resistance is emerging and spreading.

• Hospital and city wastewater treatment plants act as central mixing hubs, collecting antibiotic residues, resistant pathogens and mobile genetics from homes and clinics. Conventional treatment often fails to completely remove these contaminants, allowing resistance genes to remain in effluent water and sewage sludge.

• Livestock farms and aquaculture systems use large amounts of antibiotics, enriching resistance genes in animal gut microbes and manure that then end up in soil, crops and surrounding waters.

• Pharmaceutical manufacturing facilities can discharge extremely high levels of both antibiotics and resistance genes, increasing the risk that dangerous resistance traits will spread downstream.​

At these locations, resistance genes can hitchhike on mobile genetic elements such as plasmids, making it easier for bacteria to “swap” resistance traits and create multidrug-resistant strains.​

Why traditional monitoring is not enough

Most AMR surveillance is still focused on clinical samples, but the authors argue that environmental surveillance should be covered. Classic culture-based tests remain important because they measure whether bacteria actually survive antibiotics and provide live isolates for further study. However, many environmental bacteria cannot be easily grown in the laboratory and these methods may lose most of the present resistance.

Newer tools quickly change the picture:

• Phenotypic methods such as flow cytometry and Raman spectroscopy can monitor resistant cells and gene transfer in complex samples within hours, without the need for culture.​

• Genotyping methods such as high-throughput quantitative PCR, CRISPR-based assays, and metagenomic sequencing can detect hundreds of resistance genes simultaneously and identify which bacteria carry them.

• Long-read sequencing now allows researchers to reconstruct entire mobile genetic elements and see exactly how resistance genes are organized and move between hosts.​

“The message is clear,” said lead author Huilin Zhang. “No single method can capture the full story of environmental resistance. What we need is comprehensive surveillance that links what bacteria can do to the genes they carry and where they spread.”

One Health and smarter mitigation

The review is framed in the concept of One Health, which emphasizes that the health of humans, animals and the environment are closely linked. The authors suggest tackling AMR on two fronts: source control to reduce the amount of antibiotics, resistant bacteria and resistance genes entering the environment and process control to intercept them along key pathways, such as wastewater treatment.

Source control measures include stricter management of antibiotics in medicine and agriculture, better regulation in low- and middle-income areas, and cleaner production in pharmaceutical industries. The authors also highlight emerging “green” solutions such as enhanced biodegradation of antibiotics, the design of more biodegradable drugs, and alternative antimicrobials such as peptides and phages.

On the process side, improved wastewater treatment and waste management are vital. Conventional disinfection can reduce many resistant bacteria, but can leave resistance genes intact, especially in solid waste streams. More advanced approaches such as hyperthermophilic composting, advanced oxidation, membrane processes, nanomaterials, bacteriophage-based therapies, engineered DNA scanning bacteria, and CRISPR-based tools show promise, but require further research, safety evaluation, and cost reduction.

Focusing on the most dangerous resistance

Rather than simply counting how many resistance genes exist, the authors argue that surveillance and policy should prioritize traits that actually pose a health risk. Three stand out:

• Mobility: how easily genes move between bacteria and environments.​

• Host pathogenicity: whether bacterial hosts are capable of causing disease in humans or animals.​

• Multiple resistance: if the genes and their hosts are resistant to multiple essential antibiotics, limiting treatment options.​

“Environmental AMR is not just about how many resistance genes we can find,” said corresponding author Feng Ju. “What matters most is which genes are mobile, which pathogens carry them, and how they evolve in real-world ecosystems. That’s where surveillance needs to be focused and where mitigation will have the biggest impact.”

The authors call for global, standardized protocols that make environmental AMR data comparable across countries and over time. Without such standards, they warn, the world will struggle to identify emerging threats early enough and design effective One Health interventions that protect both people and the planet.​​