The leopard shark was still alive when it washed ashore on a San Francisco Bay mudflat a few hundred feet south of the runway of the San Francisco International Airport. A state game warden found it there, lolling in shallow brown water, dying.

The warden called the Pelagic Shark Research Foundation, a shark conservation group based in Monterey, California. The group’s executive director drove up, packed the now-dead shark in a cooler, and FedExed it to Mark Okihiro.

Okihiro is a California Department of Fish and Wildlife senior fish pathologist whose day job is to assess disease in white seabass hatcheries. But lately he has become, in his spare time, a leading expert on what causes sharks to die where people can find them. In the last few years Okihiro has examined the corpses of stranded mako, thresher, great white, leopard, and salmon sharks, and he led a state investigation into a mass die-off in San Francisco Bay in 2011 that he thinks may have involved thousands of leopard sharks and bat rays.

Although the root causes and circumstances of the strandings vary, they all seem to be the result of fatal brain infections. But while individual and mass stranding events seem to be happening more frequently and affecting more species, researchers say there’s little data and not nearly enough funding to investigate.

“We know mass stranding events have occurred historically,” says California State University Long Beach shark biologist Chris Lowe. “It’s hard to say whether these [recent ones] are driven by anthropogenic issues, or whether they’re climate issues, or a combination. And of course that’s what everyone wants to know. Are we looking at something that’s going to be more prevalent, not just in San Francisco Bay but globally?”

Rise of Brain Disease

Reports of brain disease are almost nonexistent in sharks until the last few years. In 2007 researchers found a stranded basking shark on the east coast of Scotland and identified meningoencephalitis as the cause of death, noting in a 2010 paper in the Journal of Comparative Pathology that “few diseases have been reported in any species of shark and none in the basking shark.” Other papers have mentioned brain disease in a brown shark caused by Vibrio bacteria, and in wild nurse sharks infected with nematode parasites.

In 2012 researchers identified infection caused by Carnobacterium maltaromaticum as the cause of salmon shark meningitis and subsequent strandings on the West Coast, which have been regularly reported between Baja California and the Gulf of Alaska for decades. The bacteria occur normally in the water, and in the gut of healthy cold-water fish like salmon and trout. But it is not typically present in sharks.

So for reasons researchers still don’t understand, sometimes the bacteria become pathogenic, sneaking inside a shark via the ears or nose and, Lowe says, “literally eating its brain,” causing disorientation and eventually death.

Okihiro and Laura Martinez-Steele, a graduate student in Lowe’s lab at CSU Long Beach, found carnobacterium in the diseased brains of recently stranded thresher sharks—which hadn’t been known to strand until four or five years ago. In December 2016, a mako shark washed up in Southern California, the first recorded stranding for that species. Salmon, thresher, and mako sharks are closely related, and sure enough, it was carnobacterium again.

“Three species with the same infection, all three related,” says Martinez-Steele. “It could be because now we’re studying sharks more, so we know it’s happening. But then, we have salmon shark reports going so far back, it would be logical you’d see the other sharks too. It’s hard to tell because we know so little.”

On April 8, 2017, one day before the leopard shark was recovered from San Francisco Bay, a young great white shark thrashed into the shallow water near a popular surfing beach in Santa Cruz. As onlookers held up their phones to document the scene, a group of volunteers tried to push it back into the water. But the clearly disoriented shark didn’t swim off, and later washed up dead at a nearby pier.

View Images Sharks may be more vulnerable to disease when they are closer to the shore, but there they are safer from their natural predators. Photograph by Henry Hernandez

When he opened it up, Okihiro found hemorrhages in the tissue around the shark’s brain, signs an infection had killed it. Great whites are in the same family as salmon, thresher, and mako sharks, and Okihiro expected to find carnobacterium. He did not. The white shark’s brain seemed to have been invaded by something else entirely.

Searching for a Killer

The shark strandings continued. Even as Okihiro mailed samples from the white shark to various pathology labs for further analysis, more leopard sharks started to turn up in the San Francisco Bay. A couple walking the shoreline in Foster City, a small suburb built on bay fill and carved with manmade lagoons, reported 20 dead or dying sharks on a single stretch of beach. More reports came in from Berkeley, Oakland, and elsewhere, leading to hundreds of shark deaths around the Bay by the second week in May

Okihiro took samples from the inner ear, cerebrospinal fluid, and tissue surrounding the brain of a dead leopard shark and put it in a Petri dish to see if bacteria would grow. But he saw nothing for a week, well past the point at which carnobacterium would have appeared. He began to wonder if the culprit was a virus, which wouldn’t show up in his agar plate.

But then, 10 days after he’d started it, the dish sprouted a fungal colony. Okihiro had what he calls a “patient zero.” A fungal colony showed up shortly thereafter in a dish with samples from the second leopard shark he’d analyzed.

Eight more leopard sharks Okihiro analyzed showed evidence of fungal infections, although most of them have not yet yielded fungi in the Petri dishes. Okihiro thinks that might be because they were already dead when he collected them, causing the fungi to stop reproducing. But the so-far negative result means there’s nothing definitive to say.

“Right now it’s just hypothetical,” he says. “We hypothetically believe that this fungal pathogen proliferates in stagnant water, in salt water marshes, in slow-moving salt water sloughs that meander throughout the south bay, and these manmade lagoons in Foster City and Redwood Shores.”

The die-off happens in the spring, Okihiri says, because that’s when leopard sharks typically gather in large groups in shallow water where the fungal pathogens have exploded.

In theory, Okihiro says, researchers could isolate the fungi species—it’s something in the Penicillium genus—and then look for DNA signatures from that species in preserved tissue from the 2011 leopard shark die-off. A match would allow biologists to set up a screen for the fungi in the water, to figure out when the concentration becomes lethal, and to potentially predict the conditions that might cause future die-offs.

But that’s where the investigation runs into the reality of most shark investigations: there’s just no money for it, Okihiro says, and there are still so many questions.

Conditions for Sickness?

It’s likely, for example, that California’s record rainfall played a role in causing the die-off this year, either by flushing the fungal pathogen and other toxins into the water, or by lowering the salinity of the Bay and weakening the sharks, allowing the fungus to do more damage. Or it’s possible this is just a normal disease event: strandings and mass die-offs are reasonably common in the marine world, affecting all kinds of species from invertebrates to whales. It can take years to determine what happened. (Learn about one of the largest whale strandings ever.)

It’s also possible that this is just a sign of increasing shark populations. Regulations on nearshore fishing and habitat restoration have helped both leopard and thresher sharks rebound over the last half-century. No one has studied either species closely enough to know their baseline levels. And as threats to shark populations go, even a die-off numbering in the hundreds pales in comparison to the global threats of overfishing or fishing bycatch (which kill an estimated 100 million sharks a year).

“In the last 20 years there’s been a growing number of studies of contaminants in sharks,” Lowe says. “But other fish are better studied. There are people trying to do this, but it’s very expensive. And until it becomes a serious human or wildlife problem, there’s no money.”

While the fungal pathogen killing the leopard sharks has affected them indiscriminately, the salmon, thresher, and mako sharks that have washed up seem mainly to be young. Martinez-Steele says this could mean the sharks are taking on contaminants or pathogens in utero and don’t develop the immune system strength to fight off infection in the way adult sharks might. Or it could just be, as with the leopard sharks, that we’re not yet seeing the full picture.

“Juveniles live close to the coast,” Martinez-Steele says. “It’s their nursery area. They’re protected there. Could adults be getting this too, but they’re more offshore so they’re not stranding?”

Lowe says that, given an unlimited budget, he’d try first to identify a baseline shark microbiome. Research into the world of microbes inside people has yielded amazing insights into what makes people healthy—perhaps it could help us understand what causes some sharks to get sick and strand.