There’s a lot to be learned from poop. By studying stool samples, scientists have made huge progress in understanding the microbial communities that live in our guts. They’ve even used fecal transplants to cure people with recurrent gastrointestinal infections. Now, they believe that digging through sewage might help address one of the most pressing public health crises today.

Increasingly, pathogens are resistant to the antibiotic, antiviral, and anti-fungal medications seen in our pharmacies. In many cases, these disease-causing superbugs are resistant to multiple classes — or even all classes — of the medications currently available. That means that bacteria once considered a mere nuisance can now be potentially deadly, especially for people with compromised immune systems such as cancer patients, transplant patients, and the elderly.


The World Health Organization and other health agencies have recognized the rise of antimicrobial resistance as a critical threat. Back in 2014, when the WHO came out with its first published assessment of antimicrobial resistance, then-Assistant Director-General for Health Security Keiji Fukuda said, “Without urgent, coordinated action by many stakeholders, the world is headed for a post-antibiotic era, in which common infections and minor injuries which have been treatable for decades can once again kill.”

Late last year, the U.S. Centers for Disease Control and Prevention reported there are 2.8 million antibiotic-resistant infections in the country every year, leading to 35,000 deaths. The situation is even worse in countries where antibiotic use is less regulated.

The new battle against antimicrobial resistance is being fought on many fronts. Among the ways the healthcare system is fighting back: reducing unnecessary use of antibiotics; testing pathogens faster to deliver targeted antibiotics instead of broad-spectrum ones; and raising awareness about how drug resistance spreads.


But let’s get back to poop. Public health experts desperately need to know what the landscape of antimicrobial resistance looks like to figure out how to gain the upper hand, and to predict where things may be about to get worse. Where is it happening? Against which specific therapies have pathogens developed resistance?

In a research paper published in the journal Science earlier this month, infectious disease experts from Denmark and the U.K. suggest that conducting routine DNA surveillance in sewage could deliver the information necessary to understand, at the community level, what antimicrobial resistance looks like. To be clear, this is a policy recommendation; it has yet to be broadly implemented in communities. But drastic cost reductions in DNA sequencing technology have made this idea feasible, even in low- and middle-income countries where antimicrobial surveillance has been particularly difficult. The scientists call it “an affordable surveillance option in resource-poor settings.”

DNA analysis can reveal not only which superbugs are turning up in a local population, but also which antimicrobial treatments they have developed the ability to dodge. Because bacteria can easily swap genetic elements needed for drug resistance with other bacteria, finding that a specific type of resistance is common could tip off public health officials that it may soon be taken up by more dangerous pathogens. Having a preview of imminent threats would then allow local doctors to switch to a different therapy, giving patients better chances of effective treatment while staving off the rise of resistance.

If communities start to invest in DNA sequencing for sewage processing plants, something as simple as flushing the toilet might help keep you and your neighbors healthier.