The mysterious respiratory illness that may have sickened scores of dogs across the country could be caused by a new type of bacterial infection that may be very good at evading the canine immune system, researchers say.

Some dogs have died from the illness, which starts with causes a cough that can last for weeks, runny eyes and sneezing.

In a development that might help shed light on the illness, which has affected a variety of dog breeds, researchers at the University of New Hampshire’s Veterinary Diagnosis Laboratory and the Hubbard Center for Genome Studies told NBC News they have identified a pathogen that might be what’s making pets sick. 

Through a genetic sequencing of samples from an initial group of 30 dogs from New Hampshire who were infected last year and then an additional 40 from Rhode Island and Massachusetts who got sick this year, the researchers say they have discovered a previously unknown germ.  

The pathogen is “a funky bacterium,”  said Dr. David Needle, pathology section chief at the College of Life Sciences and Agriculture at the University of New Hampshire. “It’s smaller than a normal bacterium in its size and in the size of its genome. Long story short, it’s a weird bacterium that can be tough to find and sequence.”

The germ “is new as a potential cause of disease, but it is likely to be— or to have evolved from — a component of the dog microbiome,” he said. Dogs as well as humans have multiple types of harmless bacteria and other microorganisms living both inside and outside the body. In the gut, they are thought to aid in digestion. 

The bacterium was discovered after a painstaking search. 

“After initial sequencing showed there were no known viral, bacterial or fungal pathogens, time consuming and dogged work by graduate student Lawrence Gordon showed that 21 of the initial 30 samples from New Hampshire had some genetic material from one atypical bacterial species,” Needle said. 

The UNH team is sharing its results prior to publishing a research article, hoping they will give veterinarians some information as they deal with other respiratory syndrome outbreaks, he said.  

Scientists aren’t even sure yet whether the same bug is making dogs sick across the nation. Many researchers have wondered whether it was a bacterial or a viral pathogen. One thing veterinarians do know is that the germ is something they don’t recognize.

Mike Stepien, a spokesperson for the USDA Animal and Plant Health Inspection Service (APHIS), said in an email Wednesday the agency is working with multiple state animal health officials and diagnostic labs regarding the respiratory illness in dogs that, "in rare cases, has progressed rapidly to death." 

"APHIS and partners have not yet definitively identified the cause of illness," Stepien responded in an email. "There are no reports of human illness affiliated with these cases at this time."

New Hampshire is one of a handful of states that have reported cases of the respiratory infection in dogs. 

The Oregon Agriculture Department has received more than 200 case reports from veterinarians around the state since the beginning of August, spokesperson Andrea Cantu-Schomus said in an email. A very small percentage of the dogs have died, Cantu-Schomus said.

Other states with possible cases include: 

  • Colorado
  • California
  • Indiana
  • Illinois
  • Washington
  • Idaho
  • Georgia
  • Florida

In conversations with veterinarians, Dr. Karl E. Jandrey, a professor of clinical small animal emergency and critical care at the University of California, Davis, School of Veterinary Medicine, has heard of potential cases in North Carolina, Rhode Island and Virginia, as well.

Because there is no test yet for the illness and because many of the symptoms are similar to other respiratory infections, such as canine influenza and Bordetella (kennel cough), it’s unknown exactly how many dogs have been affected. With hundreds of cases identified by symptoms reported only in Oregon, it’s likely there are thousands. 

Normally, to determine what antibiotics might work best against a particular type of bacteria, labs grow the bugs in a petri dish and then try to kill them with various medications. Needle and his colleagues have not been able to grow the new bacteria in the lab. Nevertheless, its structure offers some clues about which medications might be the best choice to fight it, he said. The antibiotic doxycycline may be effective, he suggested