Scientists Uncover Hidden Bacterial “Skeletons” Behind Lingering Lyme Disease Symptoms

Researchers uncover why the body may keep reacting to a hidden threat even long after the bacteria are gone.

As many as 20 percent of patients treated for Lyme disease continue to experience lasting symptoms. Researchers believe this may be due to lingering antigens from the Borrelia burgdorferi bacterium, similar to how residual viral particles are thought to contribute to long COVID-19. Individual variations in how the immune system responds to these bacterial remnants, particularly fragments of the cell wall, likely influence whether symptoms persist.

Lingering symptoms after treatment for Lyme disease are more common than many realize. A 2022 study found that 14 percent of patients diagnosed and treated early with antibiotics still developed Post-Treatment Lyme Disease (PTLD). These patients often report ongoing problems such as fatigue, cognitive difficulties, joint pain, and arthritis. Despite its prevalence, the medical community continues to debate the causes of PTLD and how best to treat it.

Now, researchers at Northwestern University may have identified a potential explanation. They suggest that fragments of the Borrelia burgdorferi bacterium, the pathogen responsible for Lyme disease, can persist in the liver even after the bacteria have been destroyed by antibiotics. These bacterial remnants, particularly from the cell wall, may continue to stimulate the immune system unnecessarily, causing symptoms that resemble a chronic illness.

This theory is similar to one proposed for long COVID, in which lingering viral particles are believed to provoke prolonged immune activity, said bacteriologist Brandon L. Jutras.

“Lyme and long COVID-19 are clearly vastly different diseases, but it’s possible that they share a more general mechanism of inappropriate inflammation caused by remnants of a previous infection,” said Jutras, who led the research. “The maladaptive response is a product of an infection, but perhaps not necessarily an active one in all cases.”

Peptidoglycan is a structural feature of virtually all bacterial cells and a common target of antibiotics, including penicillin. The research, recently published in the journal Science Translational Medicine, tracked the biodistribution of peptidoglycan from different bacteria, in real time, and found that all cell wall material is rapidly shed, but Lyme disease’s peptidoglycan persists for weeks to months.

Understanding Persistent Lyme Arthritis

Lyme arthritis is one of the more common long-term impacts of exposure to Lyme. If a patient has a swollen knee, for instance, it is full of synovial fluid, a natural lubricant found in joints. Jutras said his team looked at the fluid in humans and found that pieces of the peptidoglycan were omnipresent weeks to months after treatment.

“In the context of Lyme arthritis, if you give patients anti-inflammatory, disease-modifying antirheumatic drugs, they get better,” Jutras said. “Some of these very same patients do not get better after oral and IV antibiotics, which implies there is something unique about how patients respond at a genetic level.”

Jutras, who joined Northwestern faculty last summer, is an associate professor of microbiology-immunology at Northwestern University Feinberg School of Medicine and a member of the Center for Human Immunobiology at Northwestern. He has been studying Lyme disease for more than 15 years, beginning in graduate school, and was previously an associate professor at Virginia Tech University.

A Unique Bacterial Signature

“Peptidoglycan is kind of like a structural skeleton in virtually all bacteria, acting as a big protective bag for the bacterium,” Jutras said. “Penicillin, amoxicillin, and dozens of other drugs target peptidoglycan synthesis because it’s a molecule that is specific to bacteria, it has similar structural features across the kingdom, and it’s essential.”

Lyme’s peptidoglycan, however, is structurally unique, and this difference may be behind its persistence in humans. Instead of looking the same as with other bacteria, the Lyme peptidoglycan is fundamentally distinct, which is facilitated in part by sucking up sugars from its tick vector. Upon bacterial cell death, by antibiotics or the immune system, surviving molecules tend to relocate to the liver, which can’t process the modified peptidoglycan.

Without this modification, it seems likely that the peptidoglycan would clear right away, as in other infections.

“The unusual chemical properties of Borrelia peptidoglycan promote persistence, but it’s the individual patient response to the molecule that likely impacts the overall clinical outcome,” Jutras said. “Some patients will have a more robust or stronger immune response, which could result in a worse disease outcome, while the immune system of others may largely ignore the molecule. So, in essence, it’s not about whether the molecule is there or not, it’s more about how an individual responds to it.”

Jutras hopes the groundbreaking findings will lead to the development of more accurate tests, possibly for PTLD patients, and refined treatment options when antibiotics have failed. To effectively stymie PTLD, instead of neutralizing an infection that may no longer exist, efforts are underway to neutralize the inflammatory molecule, including weaponizing monoclonal antibodies to target peptidoglycan for destruction.

Reference: “The peptidoglycan of Borrelia burgdorferi can persist in discrete tissues and cause systemic responses consistent with chronic illness” by Mecaila E. McClune, Osamudiamen Ebohon, Jules M. Dressler, Marisela M. Davis, Juselyn D. Tupik, Robert B. Lochhead, Carmen J. Booth, Allen C. Steere and Brandon L. Jutras, 23 April 2025, Science Translational Medicine.

The research was supported by the National Institutes of Allergy and Infectious Diseases (R21AI159800, R01AI173256, R01AI178711), the Steven & Alexandra Cohen Foundation, the Department of Defense (TB220039), the Global Lyme Alliance and the Bay Area Lyme Foundation.