Why Salish Sea researchers are targeting superbugs in marine mammals

Harbor seals and porpoises in the Salish Sea experience antibiotic-resistant bacteria differently, pointing to worrying implications for orcas.

harbor seal in the ocean near kelp

A harbor seal in Puget Sound swims by a National Oceanic and Atmospheric Administration researcher conducting a monitoring study. (NOAA)

Antibiotic medicine has saved innumerable people, but research has shown we are prescribed antibiotics more often than needed, leading bacteria in our bodies to build up immunity and become superbugs.

The negative impacts aren’t limited to humans, though. Through a multitude of possible pathways, including runoffs, sewage and landfills, more antibiotics and antibiotic-resistant bacteria are showing up in the Salish Sea and in the bodies of the wildlife that live there — especially marine mammals. 

The ways we use antibiotics in medicine, agriculture and beyond have concerned Dr. Stephanie Norman, a wildlife veterinarian and epidemiologist with Marine-Med, for decades. It’s for that reason that Norman and a team spent two years collecting and analyzing animal necropsy samples from porpoises and harbor seals in the Salish Sea. They wanted to get a better idea of how susceptible marine mammals are to antibiotic resistance and how these bacteria spread through the world. Antibiotics might find their way into the marine environment via a host of things we medicate: people, pets or even farm animals. 

“We don't understand a lot about how antibiotic resistance moves through the environment, and what effect it could potentially have on wildlife,” says Dr. Joe Gaydos, a co-author on the study and science director of the SeaDoc Society. “We don't treat a lot of wildlife with antibiotics. But occasionally we do, with rehabilitation and things like that, and so we don't want to be causing a problem someplace where there shouldn't be a problem.”

Studies of marine animal antibacterial resistance in Puget Sound have taken place before, but they were mostly limited to single species in narrow locations. Norman can count them on one hand. Her team’s efforts are broader and more structured, dealing with more than one species across a wide geography of inland waters, with multiple age classes within those species. 

After taking samples from 95 animals — 74 harbor seals and 21 porpoises — the team found the data across age classes and geography showed significant numbers of harbor seals and porpoises host bacteria that resist treatment by common antibiotics. How that resistance unfolded in these populations in some ways flies in the face of what researchers expected to see, creating concern for porpoises, harbor seals and animals like endangered southern resident killer whales. 

“What it's showing is that stuff that we're doing on land is getting into the ocean whether we know it or not,” Gaydos says. The findings also tee up another frightening prospect: that this antibiotic resistance and ensuing superbugs could make their way back to us.

⁠The findings 

Collecting samples from wild animals is a time-sensitive science that takes a village, and Norman’s showed up for her in spades in the form of the region’s robust marine mammal stranding network. 

Norman’s sampling period, from September 2018 through June 2020, relied on stranding network members to swab the intestines and lesions of dead porpoises and seals after an animal autopsy, or necropsy. Multiple marine animal stranding networks around the Salish Sea had to be aware of animal deaths while collecting samples from beached bodies in a 48-hour window. After that, carcasses become too decomposed to be useful, with bacterial samples so overgrown that they mislead results. 

a harbor seal with a veterinary technician

An abandoned harbor seal pup received treatment at the World Vets Marine Mammal Urgent Care Clinic in Gig Harbor from Dr. Cathy King in July 2019. While harbor seals in the Salish Sea spend more of their lives near land and people than porpoises do, a research team recently discovered porpoises host more bacterial resistance. (World Vets.)

An abandoned harbor seal pup received treatment at the World Vets Marine Mammal Urgent Care Clinic in Gig Harbor from Dr. Cathy King in July 2019. While harbor seals in the Salish Sea spend more of their lives near land and people than porpoises do, a research team recently discovered porpoises host more bacterial resistance. (World Vets.)

Norman worked with Phoenix Laboratory, a commercial lab in Mukilteo, to analyze the samples. These animals harbor thousands of kinds of bacteria, many of which are perfectly benign or even helpful. So the team elected to look for some of the most common or dangerous pathogens to human and animal health, grow them in the lab and treat them with 15 popular antibiotics to analyze whether the animals hosted bacteria that couldn’t be treated by popular antibiotics. The team ultimately analyzed 144 bacterial isolates from 85 of the 95 animals sampled. 

More than a third of those bacterial samples showed resistance to at least one antibiotic. That didn’t surprise Norman, but the fact that 26% of cumulative samples showed resistance to two or more drugs caught her attention. A few were even resistant to as many as seven or eight drugs. 

"A third of these animals that are carrying around bacteria that are resistant to antibiotics, and none of them had ever been in the hospital; none of them had ever taken antibiotics or eaten beef from a food lot, right?” says Gaydos. “So it's like you start to think, ‘OK, how are these things really getting in here?’"

Researchers expected to find more drug-resistant bacteria in the harbor seals, since they spend much more of their lives on beaches and near shore, close to humans and land-based wildlife. But the data revealed that porpoises have it worse. 

“We found that there was a greater percentage overall of resistance in the porpoises interestingly, and I wasn't expecting that,” Norman says. Not only do more porpoises contain a greater percentage of resistant bacteria, they also more often contain multidrug resistant bacteria than harbor seals do overall.

stranded harbor seal on a beach with a boat in the water in the background.

World Vets responds to a stranded harbor seal reported dead on Vashon Island in February 2019. The seal was necropsied and swabbed as part of dr. Stephanie Norman's study into antibiotic resistance in marine mammals. (World Vets.) 

World Vets responds to a stranded harbor seal reported dead on Vashon Island in February 2019. The seal was necropsied and swabbed as part of dr. Stephanie Norman's study into antibiotic resistance in marine mammals. (World Vets.) 

“Porpoises are always in the water, so it tells us that [...] either it's the genes in the porpoise, or it's where they're going, or what they're exposed to, or maybe even what they're eating is different than the harbor seals,” Norman says. 

“It looks like Puget Sound has the potential to be this large environmental pool of resistance — I don't know to what degree — but it wouldn't be surprising considering it's a very urban area,” Norman says. “If they're defecating [bacteria such as] Pseudomonas out in the water, and you go swim in or eat fish from the water, I mean, it kind of makes you stop and think a little bit.”

Washington State University’s Dr. Doug Call, a professor of molecular epidemiology unaffiliated with the research, says the study adds to our understanding of the presence and spread of antibiotic resistance in places where we wouldn’t expect to see selective pressure like this. 

“We see similar patterns in terrestrial organisms where you would think resistant bacteria should be absent [such as] wildlife in northern Tanzania or Amazonian peoples in Brazil,” he says. “These findings reflect the reality that bacteria are disseminated widely and this includes antibiotic-resistant strains that originate from both human and natural sources. … It is unlikely that bacteria found in these animals pose a specific public health threat. Instead, it is one more narrative describing the potential impact of human activities on our environment.”

Dr. Rebecca Gast, a molecular ecologist with the Woods Hole Oceanographic Institution, says it makes sense to see antibacterial resistance in the marine environment, given that resistance is a natural process that can occur beyond human antibiotic use. Whether the resistance we’re seeing is due to human activity, she says, needs more research to confirm. “Not many studies have been accomplished on free-ranging, healthy marine mammals. It is difficult to say whether the resistant bacteria associated with dead, stranded animals is really different. We need better baseline data and more long-term data in order to establish whether trends exist, … where resistance is coming from and whether it can be managed,” Gast says. 

Call, however, says it’s reasonable to assume human sources more often than not — especially given how much treated wastewater comes out of cities near the Salish Sea. 

Knowing which kinds of bacteria might be resistant to different antibiotics, Norman and Gaydos say, could better help direct the course of treatment for injured seals, porpoises and even orcas. Many of the antibiotics used in animals are the same as those prescribed to humans.

“If they have a one-third chance of having bacteria that's resistant to at least one antibiotic, not only am I going to put that animal on antibiotics, but I'm gonna try and [culture] the bacteria to make sure that the drug that I use is sensitive. So it requires a little more effort on our part to make sure we're treating with the right medication,” Gaydos says. 

The orca angle

Norman and her colleagues wanted to study porpoises for a few reasons. For one, porpoises are the number one stranded cetacean in the area. It was likely researchers would be able to find enough of them in multiple age classes and geographic areas to accomplish a novel, worthwhile study. 

The second reason is more ominous: Porpoises are genetically similar to orcas, and their health tells us a lot about possible risks to the endangered southern resident killer whale population, now down to 75 animals

“They live in the same area as these whales, they occupy the same habitat, they are cetaceans, just like the killer whales, and they’re top-level predators,” Norman says. 

As more transient orcas populate the Salish Sea, porpoises can tell us what might happen to them as well. While the southern residents don’t eat the same food as porpoises, transient orcas often eat the porpoises. 

“They can serve as a warning sign. If something unusual comes up in porpoises, then at least we can let the southern resident killer whale research community know,” Norman says. 

If funding materializes, Norman hopes to continue her work by monitoring a few explicit sites around the Salish Sea. She and her team would then employ molecular source tracking from water and sediment samples to track the flow of bacteria throughout the environment and determine whether their sources are human, animal, or otherwise. 

When she and a team did source tracking related to beluga health in Cook Inlet, Alaska, they discovered the animals had bacteria that had come from animals, dogs, and cattle — the latter of which could have been cross-contamination from moose. 

“So I imagined you probably could see a lot of that kind of stuff happening aroundPuget Sound. It just hasn't been examined in great detail yet,” Norman says. 

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