Sea Sick

By Rebecca Kessler

Illustration by Steve Lawver

The whale lay dead on the concrete lab floor, all 13 feet and 1,600 pounds of him. He had washed up late the night before on a Massachusetts beach, alive but very ill. Marine biologists from the New England Aquarium made the call to euthanize him, then trucked the body 95 kilometers south to the necropsy laboratory at Woods Hole Oceanographic Institution. But this wasn’t just any whale. It was a Cuvier’s beaked whale, a rarely glimpsed species that keeps to waters more than 1,000 meters deep and is almost never spotted near the coast. Now, more than a dozen researchers from four institutions were trying to piece together the story behind its stranding.

Marine veterinary scientist Michael Moore led the necropsy, assisted by research associate Andrea Bogomolni. After inspecting marks on the skin, the team severed the head with a sharp knife and sent it into the next room for CT scanning. They then proceeded inward to dissect and examine each organ.

This was obviously one sick whale. Bogomolni noted a greenish froth and congestion in the lungs, signs of a severe pneumonia. The brain was inflamed, its blood vessels riddled with lesions, and its outer membrane hemorrhaging, indicating another serious infection.

When the lab work came back a few days later, it revealed something unexpected: a number of microorganisms normally associated with infections in humans, not marine mammals. Equally intriguing, the whale was harboring several bacterial strains that were resistant to multiple antibiotics. Did one of those eyebrow-raising bugs cause the health problems that triggered the whale’s stranding?

It’s impossible to say, but it’s clear that the unfortunate whale fits into an ominous trend. Microbes that cause stubborn infections in people are cropping up in marine animals with unsettling frequency. The study of this phenomenon is in its infancy, but researchers are zeroing in on its possible causes, which range from hospital waste to bacteria offloaded by beachgoers. They’re also starting to worry that the pathogens may be sickening species already stressed by ship collisions, dwindling prey, and other problems. And one cutting-edge line of research has uncovered a more chilling possibility: that a new, SARS-like pandemic could rise from the sea and spread among people.

Over the past decade or so, just about everywhere scientists have looked, they’ve been discovering marine animals carrying microbes that ordinarily infect people. The influenza B virus, for instance, is normally specific to humans but showed up in harbor seals in the Netherlands. Caspian seals were discovered carrying antibodies to both influenza B and human strains of influenza A. Atlantic bottlenose dolphins in South Carolina were found carrying the “superbug” methicillin-resistant Staphylococcus aureus (aka MRSA). The list goes on, and marine mammals, seabirds, fish, and plenty of shellfish are on it.

Still, no one knew how pervasive the bugs might be throughout an ecosystem. So in 2005, Moore, Bogomolni, and their colleagues began a pioneering, three-year study to see what animals in the waters along the northeastern U.S. coast were carrying. The collection effort alone was huge. Birds and mammals stranded or inadvertently caught in fishing gear were shipped to Woods Hole from up and down the coast. The team gathered samples from a shark-fishing tournament and from live animals on remote shores. They necropsied lifeless whale hulks; swabbed and swiped away at feces, blowholes, internal organs, and infected tissues; and sent samples off for culturing or genetic screening. What came back was a list of dozens of bacteria known to infect people.

For a clue to the microbes’ origins, Moore and Bogomolni’s team tested over half the bacterial strains for resistance to human and veterinary antibiotics. When such resistance shows up in force, it raises the possibility that anthropogenic contamination is to blame. The reason? Widespread use of antibiotics in medicine and agriculture has given rise to bacteria that are invulnerable to many drugs. These resistant bacteria have started spilling into the environment and trickling into a variety of species—indeed, resistant bacteria were rampant in the animals examined by the Woods Hole team.

Fifty-nine percent of the strains they tested were resistant to at least one antibiotic, and a whopping 16 percent were resistant to five or more. The star of the show was found in a harp seal with severe lung congestion: a strain of Chryseobacterium indologenes, an agent of hospital-acquired infections in people, that was resistant to 13 out of 16 antibiotics tested. (1, 2) “The antibiotic resistance piece gives it a smell of human impact,” Moore says.

Still, the team interprets its findings cautiously. Given that little is known about marine species microbiology, “it could very well be that this is normal,” says Rebecca Gast, a Woods Hole microbiologist who co-led the study.

Not everyone is so reticent. It’s hard to be when you’ve got five dead seal pups on your hands, victims of a Pseudomonas strain resistant to every standard antibiotic. The pups died this spring in the care of Frances Gulland, director of veterinary science at the Marine Mammal Center in Sausalito, California. Gulland says the center’s rehabilitation hospital took in the pups, along with almost 100 others, because their mothers had abandoned them on the beach after they were disturbed by people. The five pups developed pneumonia and blood infections, and Gulland’s team pinpointed Pseudomonas as the infectious agent. They treated the pups with several antibiotics in succession, but nothing worked.

She says she sees about ten such cases a year in marine mammals—deaths by pneumonia, hemorrhagic diarrhea, or blood infections caused by bugs that used to be treatable. The prevalence of antibiotic resistance in the offending microorganisms has convinced Gulland that they must have come from either a person or another land animal or have been exposed to drug-laden pollution.

Ten cases a year may not sound like much, but Gulland points out that many more animals may be dying at sea. And even if healthy populations can sustain a few extra mortalities, threatened ones may not. While the overall data are scant, Gulland says, the evidence on hand suggests it’s time to take pathogen pollution seriously—especially when seen in the context of other contaminants that threaten marine mammals. “If you look at how pollution with things like mercury and PCBs [has] changed over time,” she says, “by the time you realize it’s a problem it’s going to be really extensive.”

So how might these bacteria make the journey from a hospital to a whale living miles offshore? The biggest potential pathways are familiar ones: sewers and runoff. For instance, scientists recently reported that sea otters in California host a variety of gut bacteria known to infect people—and otters living near heavily populated areas or high-runoff flows had the greatest risk of infection. Freshwater runoff is also thought to deliver two land-based protozoan parasites—one shed by cats and the other by opossums—into the sea, where they have been killing otters with fatal brain disease.

But harmful microorganisms don’t have to flow down a pipe or a stream. Julie Ellis, a Tufts University ecologist who was a co-author in Moore and Bogomolni’s research, showed as much by studying the origin of E. coli strains in the feces of gulls on a Maine island. She’d tracked the gulls carefully and watched them engaging in a favorite pastime: hanging out and foraging at local landfills and sewage lagoons. Thinking that the gulls could be picking up more than just lunch, Ellis and her colleagues decided to see whether they could trace the E. coli the gulls were carrying back to the lagoons and landfills in nearby New Hampshire. They collected feces from the gulls at their island nests, and, sure enough, the E. coli strains inside bore a striking genetic resemblance to strains they gathered from the treatment plants and dumps. From there, Ellis postulates, the gulls could carry E. coli and other pathogens out onto the beaches and waters of New England and possibly on down to their Florida wintering grounds. (3)

Some of the bacterial sources are even more unexpected—and could change the way you look at your summertime beach vacation. Lisa Plano of the University of Miami’s Miller School of Medicine has shown that people can introduce microbes, including MRSA, straight into seawater by merely wading or swimming. Apparently, the water simply washes the microbes from your nose, your skin, or wherever you happen to be carrying them. “This has been going on for as long as bacteria have been colonizing people,” Plano says. “We just haven’t been looking for these things.” Even so, Plano emphasizes that there’s no reason to avoid the beach, since your chances of picking up a bug there are very low.

As for how terrestrial microbes may make their way into marine animals, there are more questions than answers. The animals could pick up terrestrial strains straight from the water or from prey. Then again, the animals could pick up marine strains that have acquired resistance to antibiotics from exposure to waste-borne drugs, microbes, or disembodied genes for resistance. Whether the animals go on to infect one another is another big unknown.

The sheer ubiquity of marine mammals carrying these bugs raises a growing concern for the health of human beings, even though cases of people being sickened from contact are rare. For starters, researchers and others who come into regular contact with marine mammals must now consider that a bite or a scratch could result in an infection resistant to a slew of antibiotics. More disturbingly, it means that the ocean is awash in potentially harmful bugs, and our own germs may be multiplying and traveling long distances inside its animals. “It’s definitely out there in lots of our top-level predators, and that means high levels of the food chain,” says Jason Blackburn, an ecologist at the University of Florida who discovered sharks and fish carrying multi-drug-resistant bacteria in Louisiana, Massachusetts, Florida, and Belize. (4) “That’s not all that far from our dinner plates.”

Put another way, we eat the same seafood and play in the same water as marine mammals. Their immune systems and symptoms are similar to ours. If they’re picking up infectious microorganisms, there’s a chance we could too. “What we do to the ocean and the animals in it, we are ultimately also doing to ourselves,” says Gast, the Woods Hole microbiologist.

This prospect of ocean-borne illness is troubling enough. But what if marine mammals are acting like petri dishes, brewing up new pathogens that could jump back to land and sweep through human populations? That’s the question Hendrik Nollens inadvertently stumbled upon last year.

A marine-animal veterinarian based at Hubbs-SeaWorld Research Institute in San Diego, Nollens and his colleagues have pushed the boundaries in figuring out how to diagnose viruses in marine mammals—and in discovering new ones. Their curiosity was piqued a few years back when they started coming across “astroviruses”—viruses known to cause nasty bouts of diarrhea in people and other land animals—during routine screenings of marine-mammal feces.

As Nollens’s team investigated the astroviruses, they discovered that five of them, from sea lions and a dolphin, appeared to be entirely new species. So the team took a closer look and found something even more intriguing: genetic evidence that one of the new sea lion astroviruses had combined with a human astrovirus. The two viruses had apparently traded genetic material when they infected the same cell inside a human, sea lion, or other host species. (5)

That’s not altogether unusual—trading genes with abandon is what viruses do, and most of the time, the swaps amount to little more than subtle genetic variation. But such encounters are also a great way to jump-start viral evolution, and every so often they supercharge virulence, with disastrous consequences for human or animal health. Nollens points out that SARS, HIV, avian influenza, and West Nile virus all started out like the astrovirus switcheroo, with one key difference: in those cases, the new genes let the wildlife strain jump to a person, ramp up its virulence, and take off to pandemic proportions.

Like the pathogens responsible for those diseases, astroviruses are fast-mutating RNA viruses. In fact, RNA viruses make up more than one-third of pathogens classified as “emerging or re-emerging,” according to one analysis. Nollens and his colleagues have since found new astroviruses in whales and dolphins and are now examining them for evidence of crossovers. And in addition to astroviruses, he says, two other kinds of marine-mammal RNA viruses have similar potential for jumping into humans.

Nollens takes pains to say there’s no imminent danger of a sea-lion astrovirus emerging from the sea and becoming a pandemic. But he argues that the ocean should not be ignored as a potential wellspring of new human diseases. And he’s not alone: Bogomolni and Moore point out that the northeastern coast of the U.S. has been identified as a hotspot for emerging infectious diseases. Here, among marine mammals, they found drug-resistant microbes known to infect people. “You can’t just be looking at land mammals if you are shopping for zoonotic diseases,” Nollens says.

It’s a relatively new idea, and most research into diseases that might make the jump from wildlife to people remains focused squarely on terrestrial ecosystems. That, after all, is where many infectious diseases have historically arisen, often in places where humans are making stark inroads into pristine landscapes and rubbing shoulders with wildlife. But the appearance of terrestrial pathogens and antibiotic resistance in marine animals may be a sign that our incursion into the sea—although often less visible—is no less intense.❧

Literature Cited
*1.     Bogomolni, A.L. et al. 2008. Victims or vectors: a survey of marine vertebrate zoonoses from coastal waters of the Northwest Atlantic. Diseases of Aquatic Organisms 81:13–38.

*2.    Rose, J.M. et al. 2009. Occurrence and patterns of antibiotic resistance in vertebrates off the Northeastern United States coast. FEMS Microbiology Ecology 67:421–431.

3.     Nelson, M. et al. 2008 Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping. Diseases of Aquatic Organisms 81:53–63.

4.     Blackburn, J.K. et al. 2010. Evidence of antibiotic resistance in free-swimming, top-level marine predatory fishes. Journal of Zoo and Wildlife Medicine 41:7–16.

5.     Rivera, R. et al. 2010. Characterization of phylogenetically diverse astroviruses of marine mammals. Journal of General Virology 91:166–173.

*This work  was funded by the National Oceanic and Atmospheric Administration’s
Oceans and Human Health Initiative




  • Bert Silverman September 1, 2010 at 8:23 am

    I enjoyed this article immensely. It opened up a perspective on the ocean that I had not sufficiently examined. Carefully written Ms Kessler reveals some troubling concerns about our relationship to marine life without resorting to hyperbolic rhetoric. Thanks


  • Emily Magnaghi September 1, 2010 at 5:50 pm

    Fantastic reporting! I was aware of this situation, but not to the extent reported. Nice concise condensing of the literature cited. As a new Marine Mammal Stranding Network biologist in California, I look for signs of infection and take precautions against contamination, but I will be taking this much more seriously now.


  • Jon Gelbard April 22, 2012 at 10:10 am

    I’m surprised to see this article miss the fact that about 75% of antibiotics are in fact used on livestock, not people.

    And in most cases, they are used to speed livestock growth, not merely to treat sick animals.

    More on this shocking health and environmental threat here:

    No doubt there are a number of sources of the antibiotic resistance reported in this article, and we need science to do the careful work required to isolate and address each source.

    However, to overlook the use of three quarters of antibiotics — a known driver of increasing antibiotic resistance — is a glaring omission from this article.

    Fortunately, NRDC and our partners are on the case, working to drive solutions:


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