The microscopic pathogens looked familiar. There was Salmonella, for example, a bacteria found in poultry and associated with food poisoning in people who eat tainted eggs, fruits, or vegetables. There was Staphylococcus, including a type common on human skin but which, if inhaled, can cause pneumonia. And there were startling fungi—weird not because of what they were, but because of where they were found.

Scientists didn't find these microbes in human blood or in something living inside a barn. They were found in the exhaled breath of killer whales that move between Monterey Bay, California, and British Columbia's Queen Charlotte Islands.

Researchers trying to understand why an endangered population of orcas along North America's West Coast has dropped to a mere 78 individuals have uncovered another way human beings may be harming cetaceans: infectious disease.

In a new study last week of the West's southern resident killer whales, scientists captured infectious agents not typically associated with whales in exhalations from the animals' blowholes. Some of these pathogens were even antibiotic-resistant. That led scientists to suspect these orcas may increasingly be exposed to dangerous microbes that are being flushed into coastal waterways by storm runoff or sewage.

"These animals spend a fair amount of time in ecosystems close to urban environments," says Brad Hanson, who oversees orca recovery for the National Oceanic and Atmospheric Administration. "Because of runoff, either directly or indirectly, there are a variety of things that may be getting into their system."

The study, published Friday in Scientific Reports, was the result of several years of sampling of whales and waters around the San Juans, a cluster of small islands near the border between the United States and Canada. Scientists tested waters they call the sea-surface microlayer, the tiny film of fluid on top of the sea where marine waters meet air, some small part of which they assumed would be captured when a whale exhaled.

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They also followed whales with a 25-foot pole strung with several upside-down petri dishes to capture the air escaping through their blowholes.

What they found was unexpected, to say the least. From the whales, they saw everything from bacteria normally found in oysters to molds associated with plant diseases to bacteria usually found in the fecal waste of land-based livestock. That doesn't mean the microbes were at concentrations that could make the animals sick. But many were pathogens that researchers didn't think would—or should—be there at all.

"We were quite surprised to see some of these," says Linda Rhodes, a toxicologist and molecular biologist with NOAA. "These were things that if they came out of our breath the doctor would think that was not good."

But figuring out what this discovery means may be as difficult as determining where these pathogens came from.

The West Coast's southern resident killer whales are believed to have numbered several hundred back in the 1800s. But through much of the 20th century they were stressed by toxic pollution and development, their chief food source—chinook salmon—became depleted, and their numbers were drained by wranglers who caught and sold the animals to marine aquariums. They were listed as endangered a dozen years ago.

Scientists since have surmised that these cetaceans, perhaps weakened by too little food, were made more susceptible to disease. But they are hard whales to study because when they die they simply disappear—scientists rarely get to study a dead orca's carcass. So researchers are left to make presumptions about the factors that played a role in each death.

Enter Pete Schroeder, an independent longtime marine mammal veterinarian who once cared for animals on behalf of the Navy. He developed this method of sampling blowhole breaths. It's deceptively simple and efficient. And it has offered the first comprehensive look at what small creatures may be living in the respiratory system of these whales.

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"We know we're running out of chinook, and the chinook are getting smaller," he says. "We're seeing increase in boat traffic and that can break up a calf and mother pair. What they eat is contaminated and the water in which they swim is now contaminated. And now we know they also carrying unusual opportunistic pathogens."

Many of these pathogens seem unlikely to be found naturally in whales or water, so some researchers suspect that culprit is sewage. The nearby Canadian city of Victoria disposes its untreated wastewater by pumping it directly into the Strait of Juan de Fuca. But it also may be more complicated than that.

Tests of the water immediately around where whales were swimming turned up entirely different types of microbes than they found in the whales' breaths.

"We couldn't show that the bacteria coming out of the blowhole was from the nearby water," says Schroeder. "We can't say exactly where it came from."

For now, scientists will use the tests to help try and build an understanding of the microbiome of a killer whale's breath. They also will be trying to develop a health profile of each remaining individual whale.