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Biotechnology and health

We can use sewage to track the rise of antibiotic-resistant bacteria

Wastewater surveillance helped us track covid. Now we can use it to tackle the "silent pandemic."

January 13, 2023
wastewater plant

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This week, a sore throat and bunged-up nose led me to break out my dusty old box of covid tests. I haven’t had to use one in a while—immunity where I live, in the UK, is pretty high now. In the last couple of years, I’ve had covid at least once, and have had three doses of the vaccine.

Of course, this particular pandemic isn’t over yet. But this week I’ve been thinking about how tools designed to help us track the virus that causes covid could help us prepare for the next one: the spread of bacteria that are resistant to antibiotics. Scientists call it the “silent pandemic.”

Antimicrobial resistance, or AMR, is already a huge problem. Researchers estimate that the deaths of 5 million people involved antibiotic-resistant bacteria in 2019. And the problem is only getting worse. The search for new antibiotics hasn’t had much success. Meanwhile the bacteria, and their drug-resistance genes, continue to spread. 

People who are infected with bacteria and viruses send these bugs rushing into wastewater systems with each flush of their toilet. So over the last few years, many countries have started searching wastewater for the virus that causes covid. These studies have helped us estimate how many people in an area have covid, and which variants might be spreading in communities. The same approach could help us understand—and potentially limit the impact of—AMR. 

Wastewater holds plenty of information about human health. You can find evidence of drug use in a community by sampling local sewage, for example. And scientists have studied wastewater to track polio outbreaks for years.

Until recently though, most of these studies were relatively small, academic endeavors. Covid changed all that, says Amy Kirby, an environmental microbiologist at the US Centers for Disease Control (CDC).

Nationwide wastewater surveillance relies on a system that is “very expensive to build,” she says. Developing such a system had previously been written off as too costly. “Covid, a true global pandemic that was so disruptive to the economy, really changed the calculus on that, and made it worth putting this initial investment in place,” says Kirby.

Now that we have wastewater surveillance systems for covid, we might as well use them to monitor other bugs—including antibiotic-resistant ones.

We are in desperate need of new ways to tackle the spread of AMR. We rely on antibiotics not only to treat infections but sometimes to prevent them, as in people who are undergoing surgery or are vulnerable to them for other reasons. But they just don’t work on bugs with genes that make them resistant to the drugs’ effects. 

“The infections that they cause last longer and can cause more damage … and they have a greater risk of death,” says Anne Leonard at the University of Exeter in the UK. We need antimicrobials to treat bacteria and fungi that infect the plants and crops we eat, too.

Kirby is leading an effort to establish a nationwide water surveillance system that will continuously look for AMR in wastewater across the US. The team will study samples collected from wastewater treatment plants, and search for bacterial genes that are known to confer resistance to antibiotics.

Kirby hopes to find evidence of bacteria that might cause infections—even if not everyone exposed to them gets sick. These bacteria could still make other people unwell. 

Bacteria are also able to swap genes with each other, even those of different species. This could allow harmless bacteria to pass their genes for antibiotic resistance on to more dangerous bugs, making them resistant to antibiotics too.

“As long as people are using a toilet that’s connected to the sewer system—and that’s 80% of households in the US—we can get information on [their] infections whether they go to the doctor or not,” she says.

Plans are underway for Europe-wide surveillance, too. In October last year, the European Commission proposed revising laws on urban wastewater treatment to include AMR monitoring. For now, the revision states that “it is necessary to introduce a monitoring obligation for the presence of AMR in urban wastewaters to further develop our understanding and potentially take adequate action in the future.”

There are a few ways this information might be used. It might help doctors decide which antibiotics to prescribe.

At the moment, many antibiotic prescriptions essentially rely on best guesses at which drugs are likely to work. In theory, doctors can swab a person with an infection and send the sample off to a lab, which can grow the bacteria and work out which antibiotics are most likely to treat it. In reality, this doesn’t usually happen. Often, doctors can’t wait the day or two it takes to run lab tests. A person who is dying of septicemia, for example, needs antibiotics right away.

The risk is that doctors will opt for what’s known as a broad-spectrum antibiotic—a powerful drug that’s capable of killing many different types of bacteria. These medicines should be a last resort, because bacteria that mutate to resist them could be dangerous—and potentially untreatable.

Wastewater surveillance might reveal which bacteria are spreading in a community and which antibiotics these bugs are vulnerable to. And if scientists notice an increase in genes that confer resistance to a specific antibiotic, they might advise doctors in the area to avoid prescribing that drug, says Kirby.

We can also use water surveillance to monitor how antibiotic-resistance genes might be contaminating the environment. “When we take a course of antibiotics, up to 90% of it is excreted … in feces or urine, and that can end up in our sewers,” says Leonard. And some of this wastewater can make its way into rivers, lakes, and the sea.

This means that not only are we potentially releasing our own AMR bugs into the environment, but we could be encouraging the development of new antibiotic-resistant bacteria in surface water and animal habitats. And these bacteria, or at least their antibiotic-resistance genes, could work their way back into people.

Leonard has been looking for antibiotic resistance in coastal waters around England, Wales, and Northern Ireland. She’s found that people who spend a lot of time in the water—such as surfers—are more likely to have antibiotic-resistant bacteria in their guts. People who bathe in the sea are “three times as likely to carry these resistant bacteria compared to non-bathers,” she says.

It's not a very nice thought. Especially because even if these bugs don’t make people sick, they can potentially swap genes with other bacteria in a person’s gut. And we don’t really know if harmful, drug-resistant bacteria of some kind will result.

My covid test was negative—I probably have a bog-standard cold. I know I also have billions of bugs in my gut and all over my body, some of which are likely to be resistant to antibiotics. I’m hoping they won’t become any of the dangerous ones.

Read more from Tech Review’s archive

The response to covid involved focus, determination, and vast amounts of money. We should use the same approach to tackle antimicrobial resistance, Maryn McKenna wrote in 2021.

By 2050, drug-resistant bacteria could kill more people than cancer. Their cost to the global economy is predicted to reach $100 trillion by then, Michael Reilly wrote in 2016.

The hunt for new antibiotics continues. Some scientists are enlisting the help of AI, wrote Anne Trafton.

Others are looking for alternatives to antibiotics. Some hope that CRISPR pills designed to make harmful bacteria self-destruct might work, as Emily Mullin reported in 2017.

Wastewater surveillance was used to track the spread of mpox (previously known as monkeypox) last year and helped scientists estimate how many people in California’s Bay Area might be affected, Hana Kiros reported

From around the web

Some good news: Uganda has declared an end to the country’s Ebola outbreak, less than four months after the first case was confirmed in September last year. (WHO)

Entrepreneur Martine Rothblatt dreams of a factory of unlimited organs—whether from genetically engineered pigs or a 3D printer. My colleague Antonio Regalado described her plans. (MIT Technology Review)

Researchers who study ancient DNA must involve the modern indigenous communities whose ancestors the DNA belongs to. Descendant communities should guide the research, to ensure that it is not “exploitative science that propagates the consequences of colonial practices,” write a group of scientists. (Human Genetics and Genomic Advances)

Ancient DNA analysis has been chosen as one of the 10 breakthrough technologies of 2023 by editors at MIT Technology Review. You can read about the others here.

The “Kraken” variant of the covid-19 virus might be the most transmissible yet, but that doesn’t mean it’s more dangerous. (Scientific American)

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