Every flush of a toilet tells a story of what we eat, the medicines we take, and the pathogens we carry. Beneath our feet, wastewater is an unfiltered diary of human health. Yet for decades, it has flowed largely unnoticed, carrying traces of the next global health threat.

During the COVID-19 pandemic, scientists began detecting fragments of the coronavirus in city sewers often weeks before hospitals reported spikes in cases. That revelation transformed wastewater into a vital early-warning system. But SARS-CoV-2 is only one chapter of a much bigger microbial narrative. The next pandemic, or the next silent killer, may already be mutating and spreading through the same pipes we ignore every day.

The Hidden Reservoir of Resistance

Sewage isn’t just dirty water; it’s a concentrated soup of microbes, genetic material, and human waste a perfect breeding ground for antibiotic resistance. When antibiotics pass through our bodies and into the sewage system, they don’t vanish. Instead, they create selective pressure that encourages bacteria to evolve and share resistance genes.

Studies published in Nature and The Lancet Microbe have revealed alarming concentrations of antimicrobial-resistance genes (ARGs) in wastewater samples from cities as different as New Delhi, Nairobi, and New York. These genes are mobile, often carried on plasmids small DNA molecules that can move between bacterial species. This means that harmless environmental bacteria can become antibiotic-resistant pathogens in a matter of generations.

In a 2023 report, the World Health Organization warned that antimicrobial resistance is one of the top 10 global health threats, causing nearly 1.27 million deaths annually. Yet much of the global surveillance still focuses on clinical settings hospitals and laboratories rather than the vast underground network where resistance is incubating before it reaches patients.

What Our Sewage Is Trying to Tell Us

The power of wastewater surveillance lies in its ability to detect what humans overlook. In 2020, before Nepal confirmed its first major wave of COVID-19, traces of the coronavirus were already detected in Kathmandu’s sewage. Similar findings occurred in Amsterdam, Boston, and Tokyo. The technology is simple but profound: by analyzing wastewater samples with metagenomic sequencing, scientists can detect viral fragments, antibiotic-resistance genes, and emerging pathogens long before people start showing up sick.

This approach has since been extended to track polio, influenza, and even opioid consumption in several countries. The U.S. Centers for Disease Control and Prevention (CDC) now operates the National Wastewater Surveillance System, which monitors hundreds of cities for signs of SARS-CoV-2 and other threats. But coverage remains uneven particularly in low- and middle-income countries, where data on resistant genes and environmental contamination are sparse or nonexistent.

From a scientific perspective, wastewater is not just waste it’s a global diagnostic network waiting to be built. If we treat it as such, it could become humanity’s early-warning radar for outbreaks.

A Dangerous Blind Spot

Despite its promise, wastewater surveillance faces an uphill battle. Many governments still treat it as an emergency-only measure rather than an integral part of public-health infrastructure. Funding often dries up once the immediate crisis fades. Laboratories lack standardized methods for sampling, sequencing, and data sharing. And because sewage crosses borders through rivers, trade, and migration a local outbreak can quietly become an international one before anyone notices.

In some developing cities, untreated wastewater is still discharged directly into rivers used for drinking, bathing, or irrigation. A 2024 UN Environment Programme review found that more than 80 percent of the world’s wastewater is released without adequate treatment. In such environments, resistant genes, viruses, and chemical pollutants interact freely, accelerating microbial evolution in unpredictable ways. What happens in one city’s sewage today could determine what infects another country’s hospitals tomorrow.

This blind spot is especially concerning as climate change alters rainfall patterns and floods sanitation systems, spreading contaminated water into new communities. Rising temperatures further accelerate microbial growth and horizontal gene transfer. The intersection of climate change, urbanization, and microbial adaptation could create a perfect storm one that our current health systems are not built to weather.

Turning Sewage into a Shield

To prevent that future, policymakers must stop seeing wastewater as waste and start seeing it as data. Three steps could change the trajectory:

1. Build global wastewater surveillance capacity.
Every nation should integrate sewage monitoring into its public-health strategy, supported by international partnerships such as the WHO’s Tricycle Project. The cost is small compared with the billions spent once a pandemic begins.

2. Share data across borders.
Pathogens don’t need passports. Real-time, open-access databases could allow scientists to compare resistance and viral-sequence data worldwide. The model already exists in genomic networks like GISAID for flu and COVID-19 itjust needs to be extended to wastewater.

3. Invest in waste treatment and regulation.
Advanced sewage treatment facilities should become as essential as hospitals. Pharmaceutical residues and antibiotic-rich effluents from hospitals, farms, and factories must be filtered before they enter the environment. Without such intervention, the “One Health” approach recognizingthe interdependence of human, animal, and ecosystem health remains only a slogan.

Science Needs a Megaphone

As a microbiologist studying antibiotic resistance in wastewater, I’ve seen firsthand how much valuable information we throw away. Beneath the surface of a single sewage sample lies a snapshot of a city’s health: which antibiotics people are overusing, which resistant genes are spreading, which viruses are mutating. Yet many policymakers still think of wastewater surveillance as experimental, not essential.

Scientists need to speak beyond conferences and journals. We must communicate the urgency of what we find that every untreated drain is a potential breeding ground for the next pandemic, that resistance doesn’t emerge in isolation, and that prevention is cheaper than reaction.

A Race Against Time

Pandemics are not sudden shocks; they are slow-building waves we often refuse to see coming. Wastewater gives us a chance to see those waves before they crash. But every day we delay building a global monitoring system, the tide rises a little higher.

If we choose to listen, our sewage can tell us where the next pandemic might begin. If we don’t, it will tell the story after it’s too late.