A potentially fatal mystery illness in dogs is spreading in the US. It starts with a cough.

Update:
Scientists at the University of New Hampshire may have identified a pathogen that has sickened possibly thousands of dogs and killed some of them across the country

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.

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.

“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.

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."