How a wildlife biologist became a plague-chaser in the American Southwest

FLAGSTAFF, Ariz. — When there’s a suspected outbreak of plague in this college town among the pines, the authorities know to call David Wagner. He’s a tall man, with the square-jawed looks of the sheriff in a spaghetti Western, and one of his jobs is to determine whether these flare-ups are indeed caused by the same bacteria as the Black Death. He pulls on long pants and long sleeves — preferably white, so it’s easier to spot the dark speck of a flea — and drives out to the scene.

Usually, the corpses are already underground, not because they’ve been buried, but because they are prairie dogs. In the throes of plague, they crawl down into their burrows to die at home. Wagner isn’t there for their bodies. He’s more interested in the fleas that transmitted plague in the first place. Sometimes, like their dead hosts, they too are beneath the earth, and he needs to coax them out. At other times — when he’s investigating what he’d call a “hot site” —  the blood is gone from the corpses, the fleas have begun to starve, and they’ve jumped their way to the surface to wait for another mammal to pass by. “You can just see them popping around looking for something to feed on,” Wagner said. “It’s pretty creepy.”

The creepiness stems in part from the fact that a bite, left untreated, could give Wagner lumps the size of chicken eggs; make him bleed from his mouth, nose, and rectum; turn his extremities a gangrenous black; and kill him within days. The prospect doesn’t worry him much. He carries prophylactic antibiotics, which he’ll take if he starts to feel his muscles aching or his throat getting sore. He wears latex gloves. And really, more than a liability, his access to fleas full of plague is an opportunity. It’s one of the perks of living in Flag, as the locals call it, much like peering into the Grand Canyon after just 90 minutes in the car, or eating chilaquiles at MartAnne’s.

For his good fortune, Wagner, 46, has prairie dogs to thank — and the local public health department. Unlike most Americans, these officials know that plague is still alive and well in the American Southwest — on average, there are about seven human cases a year — and that the disease can be easily treated with antibiotics if caught early enough. They also know that many of these people get infected through a fleabite, sometimes acquired at the top of a decimated prairie dog colony.

So they’ve made a deal with Wagner. The environmental health staff texts or calls him when they notice a prairie dog die-off, and, within 48 hours, at no charge, he tests their fleas for plague in his lab at Northern Arizona University’s Pathogen and Microbiome Institute. In return, the agency will hold off dusting the empty burrows with insecticide until Wagner has collected some fleas for himself.

These insects are also sacrificed in the name of public service — but this time, it comes with federal funding. The Departments of Defense and Homeland Security are interested, Wagner explained, because inside those flea intestines lie an untapped stash of “good potential weapons.” He paused, and then corrected himself. “Good … if you wanted to make a bioweapon.”

After all, if Wagner could find the bacteria, so could others. These microbes are deadly. If they get into the lungs, they can be spread person to person. Knowing the intricacies of their genomes is a form of disaster preparedness.

The government’s concern about plague, and Wagner’s interest in it, might come as a surprise to most — namely because they don’t realize the disease still exists. The last they heard, it had wiped out about a third of Europe in the 14th century, and that’s where the story ended.

But Yersinia pestis stuck around. Like many Americans, it arrived in the U.S. in the belly of a steamship at the turn of the 20th century. It’s thought to have spread east from San Francisco, leaping from seagoing rats into native rodents, hitchhiking across hills and grasslands in the guts of fleas. It arrived in other ports, too — New Orleans, Galveston, Seattle — but it was in the Southwest that it settled down. It’s hard to know for sure where it lives between flare-ups: Specialists posit mysterious groups of rodents that harbor the disease but don’t all die off. Often, it remains unseen. Rodents tend to be secretive creatures, nosing around at night, living and dying without being noticed.

Prairie dogs are the exception. They’re diurnal. They’re cute. They scamper in and out of burrows. They produce nasal, high-pitched squeaks — like a badly played oboe or a seabird’s cry, depending on your mood. And they are everywhere in a town like Flag: by the railroad tracks, on highway medians, in public parks and backyards and old cemeteries. People notice when a whole colony disappears.

The chances of getting plague are still about as remote as they can be. Americans are struck and killed by lightning, on average, more than four times as often as they get infected with plague. And if they do get infected, Wagner pointed out, they can be treated with “the same thing we give kids for acne: doxycycline.”

But if it turned up in Massachusetts or Minnesota, chances are doctors wouldn’t recognize it fast enough. Even in Arizona, they don’t always. At the beginning, plague looks a lot like a cold or the flu. In 2007, a National Park Service biologist found the carcass of a mountain lion he’d been tracking through the Grand Canyon, carried it home to perform a necropsy in his garage, and fell ill three days later. He showed up to a local clinic, nauseous and feverish, and was sent home with a diagnosis of “viral syndrome.” He was found dead not long after, his lungs full of frothy liquid and traces of plague DNA.

Misdiagnosis isn’t the only risk. Plague arrived in Madagascar much the same way it did in the U.S. — in fleas on rats in boats — but once on the island, it took off. There has been an outbreak there almost every year since 1980, according to the World Health Organization. It’s hardly the country’s most dangerous scourge: Residents are much more likely to die of respiratory infections, strokes, diarrheal diseases, heart disease, malaria, or HIV. But in 1995, a 16-year-old showed up in the district of Ambalavao with plague that could survive eight antimicrobials. The same year, another resistant strain was found, this one to a single common antibiotic.

The resistance probably came from another kind of bacteria. Germs can hitch themselves together and swap genetic bits the way you might trade gossip at a party.

In plague, it’s the kind of trick that makes bioterrorism experts nervous. After all, the bacteria were being used as weapons long before anyone even knew to call them bacteria. Plague-infected corpses were catapulted over walls. Venetians plotted to distill deadly liquid from swollen lymph nodes. Japanese planes sprinkled a rainfall of infected fleas. If those with nefarious motives and technical expertise wanted to weaponize the bacteria today, they could.

That’s where Wagner comes in. Nabbing plague from prairie dogs and bringing it back to a Biosafety Level 3 lab allows him and his colleagues to find molecular fingerprints that could potentially be used to tell apart wild plague from the lab-grown stuff. And that’s just one section in the genetic reference library of plague that he’s compiled.

“He is very famous,” said Gerardo Suzán, a professor at the National Autonomous University of Mexico, who has done research on plague. “His work is very important to track the disease in history.”

Scientists who study potential bioweapons find themselves in a bind. The worse a disease is, the better it could work as a weapon. The harder it is to handle, the more some researchers want to get their hands on it.

They are sharply aware of the contradiction.

That was apparent on a May morning while Wagner was having breakfast with Joe Busch, an associate lab director at the Pathogen and Microbiome Institute. Wagner had just gotten back from Puerto Rico, where he’d been hired to look for a bacterium called Burkholderia pseudomallei — a second-tier bioterrorism threat that, like many of these agents, was lurking in the wild. Busch had just gotten a call with some preliminary results.

“No positives?” Wagner asked, looking up from his plate when Busch got back to the table.

“Not yet,” Busch said, “I’m hoping, I’m hoping we get some good stuff.”

“I’m hoping not,” Wagner said. “That would be good for Puerto Rico.”

Busch thought for a second, as country rock wailed in the background. “Would be,” he said. “But if it’s there, it’s better if we find it.”

Being a wild-plague wrangler sounds like the fulfillment of a kid’s Jane Goodall dreams, with some microbiology thrown in. But Wagner wasn’t really dreaming those dreams as a kid. Instead, he was running around his parents’ farmland in southern Illinois, looking for arrowheads, collecting mushrooms, splashing around in creeks. He helped bale alfalfa, surrounded by its dusty summer smell. His father was an electrician, and his mother was a homemaker, and, when he thought about jobs at all, he imagined being a high school teacher. “No one in my family had really been to college, so there wasn’t a lot of information about how to do that,” he said. “So I was going to be a teacher, modeled after my favorite teacher in high school: I was going to be a physics and math teacher.”

But he didn’t much like physics, it turned out. He switched into biology, and discovered a whole subculture of summer jobs that appealed to a freewheeling farm-boy like him. Fieldwork can be at once tedious and involved — professors and grad students need extra hands, willing to work among snakes, in bug-filled brush, with only occasional showers — and Wagner joined their unshaven ranks.

In Nebraska, he measured small mammal abundance along the Platte River, using snap-traps and carting corpses back for the natural history museum. In New Mexico, he studied the prey of the Mexican spotted owl, catching voles and woodrats so he could slip them in bags and weigh them, still wriggling, with a clip-on scale. “It was like Christmas,” he said. “You walked up next to a trap that was closed, and it was really exciting because you never knew what was inside.”

He spent a summer killing birds for science, in the Wichita Mountains of southwestern Oklahoma, where cowbirds lay their eggs in the nests of the endangered black-capped vireo, leaving the rightful chicks little chance to survive. His job was to check big funnel traps that had been supplied with seed and a live cowbird — its gurgling song was bait — and then to do away with the avian parasites that flew in. He did it with his hands, using “something called a thoracic squeeze,” he said. “You just kind of squeeze them around the midsection, and keep squeezing until they suffocate. Then I used to take ’em back to the bunkhouse where we stayed and throw ’em in the freezer next to my frozen pizzas.”

He loved it. Afterward, he tried Americorps, helping out farmers in Iowa whose croplands had been flooded, but he missed his youthful days of bird-squishing and squirrel-measuring. So, like any other sensible soul pining for the great outdoors, he went to grad school. And that’s where, a few years later, he encountered plague.

The first thing Wagner noticed was that his study subjects were dying. It was the summer of 2000, and for his Ph.D. thesis, he was traipsing around in search of some 270 prairie dog colonies previously mapped by biologists. Wagner wanted to see if those populations were still active. Like most dissertations, his was partially the product of chance: “I knew I wanted to work on wildlife, and this was local wildlife.”

Not only were many of these colonies no longer active; some were dropping dead in front of his eyes, as he planted pink flags to delineate the edges of their territories. He knew that, in the past, the federal government had poisoned prairie dogs all over the West, in a misguided attempt to make room for grazing — “there is an old wives’ tale that cattle break their legs in prairie dog holes,” he explained — and that ranchers sometimes shot them, too. He didn’t see signs of either. But he did see definite signs of plague.

Then, in 2001, everything changed. Wagner had just spent another summer avoiding rattlesnakes and mapping colonies when at least five envelopes containing anthrax spores were mailed out to journalists and senators. Five people died from inhaling the bacteria, six more were sickened in the same way, 11 absorbed it into their skin, 35 more showed signs of exposure, and some 10,000 were preemptively treated with antibiotics.

To trace the source of the attack, the FBI needed to know what strain of bacteria was used — and sent samples to Northern Arizona University, where a former soybean geneticist named Paul Keim had helped figured out how to tell anthrax lineages apart.

Keim had done similar work on plague, and Wagner was already talking to him about the disease. And just as the 2001 terror attacks sent seismic waves through American immigration policy and foreign relations, similar vibrations were felt at the lab bench.

“All of sudden there was a lot of research funding to study these agents,” recalled Wagner. “Now all of a sudden everybody and their brother was becoming a biodefense researcher, following the money, sort of like what happened with Ebola, what’s happening with Zika.”

Plague was a Category A biological agent — meaning it was on the federal government’s most wanted list of potential bioweapons to study — and Wagner had just watched it sweeping through his prairie dog colonies like a cold through a kindergarten.

On a blustery day in May, Wagner and Busch drove out to the site of a recent plague outbreak where they had collected fleas. You might have expected them to head out into the wildest stretches the Coconino National Forest has to offer; instead, they pulled in behind a hotel on the eastern side of town. Then, they walked down a set of steps into a grassy triangle that served as a dog park and picnic spot. There were a few patches of bare earth, each one surrounding the mouth of a tunnel.

To collect plague-infected fleas, Wagner and Busch use a homemade contraption that looks like a metallic lasso. The components come from the hardware store: just an alligator clip soldered onto the end of a sewer-snake that you might use to clear blockages too serious for the plunger. On the end of it, they clip a white swatch of flannel, which becomes a kind of surrogate mammal. They breathe on it, to make it seem like it’s just exhaled, and then send it down the hole. “Essentially, you’re presenting them with an alternative host,” said Wagner.

Whatever fleas were clinging to the cloth would be sealed into a Whirl-Pak bag, and brought back to the lab, where they’d be picked off. For Wagner and Busch’s research, the plague bacteria inside those fleas would be isolated behind the locked doors, and then grown in a mixture of sheep’s blood and an algae-derived jelly called agar.

That was what they did for a paper that came out in 2015. “You let them grow for 48 hours, you transfer a little bit of that culture into a fresh tube of broth, and that process was repeated 60 times,” said Helen Kreuzer, a microbiologist at Pacific Northwest National Laboratory, who collaborated with Wagner on the study.

The goal was to see if a coddled life in the laboratory left any telltale marks on wild Yersinia pestis. And it did: The ancestors and descendants differed in their expression of a number of proteins.

Krezuer is no stranger to working on organisms from the wild: She herself, when not focused on biodefense research, has studied how certain single-cell organisms in Yellowstone’s acidic hot springs get their carbon. That’s just the strange, everyday ecology hidden inside any number of labs: a prairie dog expert collaborating with someone fascinated by hot-spring chemistry on a national security project partially funded by the Defense Threat Reduction Agency. A soybean geneticist, sought out by the FBI to help solve crimes.

In some ways, it’s unremarkable: collaborations form, researchers pivot, unrelated organisms end up intertwined. The local health department’s deal with Wagner was largely pragmatic. “It started with a need,” said Marlene Gaither, the environmental health program manager at the Coconino County Public Health Services District. Before that, the department had been sending fleas to the Centers for Disease Control and Prevention, “but because they cover the entire U.S., their response time wasn’t as quick as what Dr. Wagner’s lab could offer.”

Speed was especially important at the colony near the hotel. “We rolled up on this place and there were people hanging out down there walking their dogs,” said Wagner. One couple was relaxing on the grass. It was a beautiful day out — sunny, not too hot — and Wagner and Busch were happy to be outside. They could see, though, that these were “hot burrows,” with fleas jumping, their reddish bodies catching the sun. They worked quickly. The health department, they knew, was waiting.

“They gave us a chance to flag fleas for a few hours, and then we met them, and it was the changing of the guard,” he said. They had the fleas they needed. The ones that were left, popping around, hoping for a blood meal, would succumb to the health department’s dust.