We did it! Sewer District’s top-notch lab can now test for raccoon DNA

They’re cute. They’re annoying. They’re everywhere. And everywhere they are, they poop. Until now, there was no way to know when raccoons were partly to blame for E. coli trends in our waterways. So we figured out how to test for their DNA.

A raccoon in a stream.

It’s been possible for years to differentiate between human and animal sources of E. coli, and to specifically identify sources like white-tailed deer, gulls, and geese. And that’s great. Those critters are all over the place, and they’re big-time poopers.

But nobody had figured out how to test water for raccoon DNA, until Sewer District Biologist Justin Seikel did exactly that.

Japan helped — although not the entire country (which also has a big raccoon problem, by the way). Justin found a Japanese research paper that included a huge raccoon-specific gene, and that’s what he used to begin developing his raccoon test back in 2022.

Justin Seikel speaks to tour participants in front of some charts in the Sewer District lab.
Biologist Justin Seikel at Clean Water Fest, the Sewer District’s signature annual event. He’s explaining how the District’s National Environmental Laboratory Accreditation Program (NELAP)-certified lab conducts research.

The big deal about E. coli

As it happens, while E. coli can certainly make people sick — especially young children, the elderly, and people who are immunocompromised — it’s far from the baddest gut bacteria around.

But it is designated by the EPA as a fecal indicator bacteria. Because when there’s a lot of E. coli in the water, plenty of much worse gut bacteria are floating around, too.

To keep people safe — particularly in summertime, when everybody’s at the beach — it’s really important to keep tabs on E. coli. (We talked here about how the Sewer District takes on beach-water monitoring and provides daily beach safety updates during summer.)

A painstaking search

Identifying a genetic string that would always match up with raccoons (and would not falsely identify other species) took meticulous work.

To be frank, it meant getting a lot of raccoon poop into the lab — and a bunch of folks really stepped up: Our own people in the field, area rescue centers, and even the Cleveland Museum of Natural History all contributed raccoon poop to the cause.

Justin compared the DNA from the Japanese research paper with the DNA he sequenced from all those raccoon poop samples, and he identified four or five possible common sequences.

Using the National Center for Biotechnology Information, a database of sequences, Justin then isolated one particularly promising genetic sequence and proceeded to test the heck out of it.

A fantastic result

Over the past year, Justin estimates he’s tested the poop of at least 50 different animals, and the results have been utterly consistent.

“Every result has validated that my marker is specific to raccoon.” — Justin Seikel

Of course, this isn’t the end of the story: It’s time to start testing water samples — a lot of them — where raccoon contamination is suspected. And it’s time for other labs to test Justin’s test.

At the risk of introducing a metaphor that arguably has no place here whatsoever: We’ve taken the football wayyyyy down the field. Who wants to help carry it into the end zone?

Because what’s at stake here isn’t the glory of winning just one game; it’s the possibility that we’ve devised a play that could help us keep winning, as we strive to make the environment cleaner and keep people safer.



Northeast Ohio Regional Sewer District

Official Medium channel of the Northeast Ohio Regional Sewer District in Cleveland, OH