On a Friday evening in mid-January, Jackson, a five-year-old chimp living at Tacugama Chimpanzee Sanctuary in Sierra Leone, alarmed his keepers by ignoring his dinner. By Saturday, he was lethargic and having seizures. Jackson has improved since then—he is eating and seems stable, despite lingering diarrhea—but his survival is by no means guaranteed. “The disease is very much like that: you see ups and downs,” says veterinarian Andrea Pizarro, general manager at Tacugama. “One day they’re very good, the next, they’re very bad.”
Jackson has epizootic neurologic and gastroenteric syndrome (ENGS), a mysterious ailment that has killed 59 of the 60 Tacugama chimps that have come down with it since 2005. After struggling to pinpoint the cause of the disease for years, scientists and veterinarians finally have a possible culprit: a newly discovered species of Sarcina, a type of bacteria commonly found in the environment and occasionally associated with gastrointestinal disease in humans. As the researchers report on February 3 in Nature Communications, the finding suggests that some Sarcina species may in fact be highly virulent but, until now, have not been recognized.
“Maybe there’s this range of different Sarcina that look the same but have gained genetic properties that allow them to be more pathogenic,” says lead study author Leah Owens, a veterinary and doctoral candidate at the University of Wisconsin–Madison. “That can have repercussions for human and animal health.”
Tacugama is the only sanctuary in Sierra Leone for western chimpanzees, a critically endangered subspecies whose range once stretched across West Africa, but is now confined to eight countries. Located eight miles southeast of Freetown, on the edge of the Western Area National Park, the accredited, award-winning sanctuary also carries out environmental education, ecotourism and community conservation projects. Ninety-nine chimps permanently reside at Tacugama today. Many of them were rescued as babies from the illegal wildlife trade.
Tacugama’s chimps began coming down with ENGS in 2005, although it took years for veterinarians to realize that the animals they were losing had died of a common cause. The syndrome plays out differently in different individuals, with some showing neurological signs such as lack of coordination and seizures, and others suffering gastrointestinal distress—or both. Some animals seem to recover from ENGS, only to succumb weeks or months later, while others simply drop dead without any warning signs.
Tacugama’s veterinarians pursued several red herrings, including a virus that causes neurological problems, for which they vaccinated every chimp at the sanctuary. They also undertook an exhaustive removal of a poisonous plant found in the chimps’ enclosure. But cases kept coming. In 2016, the Pan African Sanctuary Alliance, an umbrella organization for the continent’s primate sanctuaries, reached out to epidemiologist Tony Goldberg, Owens’ advisor at the University of Wisconsin–Madison. Goldberg was immediately intrigued. “This is an unknown infectious disease that poses a serious risk to the health and survival of an endangered species, which happens to be our nearest relative,” he says.
It took two and a half years to get permission to export the chimp samples to the U.S. (not the least because the Ebola outbreak was underway at the time), and to work out the logistics for safely shipping them. In the end, the Wisconsin researchers obtained tissue, blood, serum and fecal samples from 19 chimps that had died of the syndrome and 14 healthy ones. “One night I came into the lab, and we had this [shipment] full of liquid nitrogen,” Owens says. “Tony was elated, like, ‘Oh my God, I’ve waiting years to look at these brains!’”
Owens, Goldberg and their colleagues performed a comprehensive analysis on the samples to characterize all of the viruses, bacteria and parasites present. Several of the samples “just had an insane number of reads for this one bacterium, like 90-plus percent,” Owens says. Diagnostic sequencing and statistical analyses confirmed that the bacterium was not present in any of the healthy chimps, suggesting a link to ENGS.
By appearance, the microbe seemed to be Sarcina ventriculi, which looks a bit like a four-leaf clover and is ubiquitous in water and soil around the world. The species was first discovered in a 19th-century human patient who presented with vomiting, but it then largely disappeared from the scientific literature related to disease. Genome sequencing revealed, however, that the team had not found S. ventriculi, but a completely unknown Sarcina species, which the team named Sarcina troglodytae. “In all the decades knowing this bacterium exists, the medical community never appreciated that what they had been calling S. ventriculi might actually be a group of related bacteria,” Goldberg says.
Chimps are not the only primates recently coming down with Sarcina. Since 2010, there has been a surge of cases of the bacterium turning up in human patients, often ones that have undergone bariatric surgery, mostly in the U.S. Clinicians have primarily diagnosed S. ventriculi based on appearance rather than genetics, however, making it impossible to say which species people are actually being infected by. But some human cases of Sarcina infection, including one fatal one, have presented with “eerily similar” effects to those seen in chimps, Owens says.
“The question is: Is this an emerging new pathogen that is different than the Sarcina we think we know?” she says. “Or is there something about the host that’s changing, that’s allowing them to get infected and sick from this?”
Owens and Goldberg hypothesize that there is a diversity of unrecognized Sarcina species, some of which are benign and some of which are opportunistic pathogens. The challenge, now, will be to untangle those different species, determine how the virulent ones are causing disease and tease out which environmental triggers inside or outside the body predispose certain primates to infection. Answering these questions could not only help protect an endangered species but people as well. As Owens says, “Chimps are basically us, genetically.”
The findings also raise questions—and hope—for how to best go about treating Tacugama’s primate residents for ENGS. “This study represents a starting point to guide further investigations in the unfortunate likelihood of future cases, and offers ideas for tailoring treatment interventions,” says Livia Patrono, a veterinarian and postdoctoral researcher in primate infectious disease at the Robert Koch Institute in Berlin, who was not involved in the work.
Already, Tacugama’s veterinarians are changing their approach to treatment. Jackson, unlike any infected chimps before, is being given probiotics and a special diet, in addition to targeted antibiotics. “Before, we were lost, trying to focus on everything,” Pizarro says. “Now we know what we have to protect against.”