Sequencing the Clues Behind a Mystery Canine Respiratory Disease

A New Question in Canine Respiratory Health

Respiratory infections are familiar to many dog owners, often grouped under the umbrella term “kennel cough,” which can include coughing, sneezing, nasal discharge, and difficulty breathing when the deeper tissues are affected. But when an unusually long lasting and medication-resistant form of canine respiratory disease began appearing across the United States in late 2022 and early 2023, veterinarians, researchers, dog owners, and the AKC Canine Health Foundation recognized that the situation called for careful scientific investigation.

Dr. David Needle, a veterinary pathologist at the University of New Hampshire, began studying samples from affected dogs to better understand what might be contributing to the disease. His team collected nose and throat samples from veterinary clinics and analyzed the genetic material found in those samples.

What they found raised an important new research question. The DNA associated with the mystery disease did not match known canine respiratory pathogens. Instead, it appeared similar to a bacterium found in humans. Dr. Needle described it as a “small bacterium with a relatively small amount of genetic material” and noted that it appears to be a new addition to the canine respiratory microbiome, the community of microorganisms that naturally live in a dog’s respiratory tract.

Studying BARDiD, One Genetic Clue at a Time

With support from the AKC Canine Health Foundation, Dr. Needle received more than $300,000 in funding to study the genetic makeup of this potential new pathogen and compare the respiratory microbiomes of healthy dogs and those with canine infectious respiratory disease complex, or CIRD.

In a 2025, Dr. Needle shared early results from an analysis of 60 samples that tested positive for the newly identified pathogen, now called BARDiD, short for “bacteria associated with respiratory disease in dogs.” The data suggested that BARDiD is a divergent species with genetic similarities to a human respiratory pathogen discovered in 2021 called IOLA, or “Infectious Organism Lurking in human Airways.”

This work has required persistence. Dr. Needle explained that one key challenge is that BARDiD cannot be grown in the lab. As a result, his team has had to rely on getting the pathogen from nasal swabs, which can contain a complex mix of material, including other microorganisms living in the nose as well as DNA from the dog’s own nasal cells. That background “noise” makes it harder to detect BARDiD specifically.

The challenge is compounded by the fact that BARDiD and other respiratory pathogens are often more concentrated deeper in the respiratory tract, such as the trachea and lungs. Because nasal samples are more indirect, finding clear evidence of the organism there can be even more difficult.

A New Sequencing Approach for a Difficult Bacterium

To move the study forward, Dr. Needle’s lab used ARTIC, a DNA sequencing protocol originally used for Ebola genomics. The team adapted this approach for BARDiD and is calling the method BARCTIC. According to the source material, this makes BARDiD the first bacterium to be sequenced with ARTIC.

“We are on target to complete the study by the end of June,” Dr. Needle told the Foundation recently. “And when we finish analysis of this final data, hopefully by the end of the year, we’ll be able to publish the whole genome of the potential new bacteria in dogs.”

The sequencing is now complete, and Dr. Needle shared, “We’re really really close to what one anticipates to be the full coverage of the genome.”

As the data are fully analyzed, the results may help researchers, pharmacologists, diagnostic laboratories, and clinicians better understand this unusual bacterium. Dr. Needle noted that the genome “could give pharmacologists a target.” He also said that respiratory pathogen PCR panels may eventually include BARDiD, which could help veterinarians understand “what not to treat them with” when a dog tests positive.

This is the step-by-step work of outsmarting infection: asking better questions, developing better tools, and using research to help the veterinary community understand what dogs are facing. With continued support, CHF-funded science can help uncover the microbial clues that shape canine respiratory health and move the field closer to answers.