For people with encephalitis, rapid treatment of their acute brain inflammation is critical for avoiding devastating physical and cognitive deficits. But appropriate treatment requires identifying the culprit causing the symptoms.

Specimens in the Mayo Clinic Neuroimmunology Laboratory after testing.

For years, the prime suspects were infections, particularly those caused by the Herpes simplex virus and mosquito- or tick-borne pathogens. But in the past decade, Mayo Clinic has been at the forefront of demonstrating that encephalitis can also be caused by the body’s immune system attacking the brain. This “autoimmune encephalitis” has been considered much less common than encephalitis resulting from an infection.

Now, in a groundbreaking population-based study, Mayo Clinic has found that autoimmune encephalitis is as common as its infectious disease counterpart. The finding underlines the need for precise diagnostic testing for people with encephalitis, as the autoimmune and infectious diseases require different treatments.

Eoin Flanagan, M.B., B.Ch.

“When physicians see a patient with encephalitis, it’s very important to test for an autoimmune cause in addition to considering infections,” says Eoin Flanagan, M.B., B.Ch., an autoimmune neurologist at Mayo Clinic in Rochester, Minnesota, and the study’s senior author.

“If an autoimmune cause isn’t considered, the patient may not receive immunotherapy. That can be detrimental—as patients often respond well to immunotherapy, but the longer the delay in receiving it, the worse the outcomes.”

Mayo Medical Laboratories offers an Autoimmune Encephalopathy Evaluation (Test ID: ENS1/ENC1) to test for autoimmune encephalitis. Dr. Flanagan notes that physicians ordering the panel should submit both patient serum and cerebral spinal fluid samples when highly suspicious.

“We need to test both because some antibodies are better picked up in serum and others in the spinal fluid,” he says. “These patients are often very sick. We do a comprehensive analysis upfront because rapid diagnosis and treatment result in better outcomes.”

Clinical Laboratory Technologist Steven Brady, MLS(ASCP), monitors results from the flow cytometry testing platform within the Mayo Clinic Neuroimmunology Laboratory.

Heavy Disease Burden

Encephalitis can cause considerable morbidity with patients experiencing confusion, altered consciousness, memory loss, seizures, and movement disorders. Hospitalizations for the disease cost $2 billion in the United States in 2010.*

A laboratory technologist prepares specimens in one of Mayo Clinic's neurology-specific laboratories.

Timely immunotherapy can often help patients regain function. “But depending on the antibody involved, recovery can be quick in the order of weeks or be prolonged and take more than six months,” Dr. Flanagan says.

Previous epidemiology studies of encephalitis have focused mostly on infectious causes, with “immune-mediated” syndromes occasionally analyzed as a subgroup. Mayo Clinic’s study is the first to determine the epidemiology of autoimmune encephalitis at a population level.

To identify cases of encephalitis, the study used data from the Rochester Epidemiology Project, a medical-records database of all medical providers in Olmsted County (where Mayo Clinic’s campus in Minnesota is located). In that study population, the prevalence of autoimmune encephalitis was 13.7 cases per 100,000 people, compared with 11.6 cases per 100,000 people for infectious encephalitis.

“Extrapolating our results to the world population suggests that about one million people are affected with autoimmune encephalitis,” Dr. Flanagan says. “The disease burden for autoimmune encephalitis—a condition that just 10 years ago went unrecognized—is significant.”

The study also found a nearly three-times higher incidence of autoimmune encephalitis for African-Americans: 38.3 cases per 100,000 people in the population group, which is largely of northern European descent. That finding is consistent with previous Mayo research showing a predisposition for certain other autoimmune neurology disorders among African-Americans. The researchers note that further studies are needed in populations with a higher proportion of African-Americans. 

Divyanshu Dubey, M.B.B.S.

In this epidemiology study, the researchers took several steps to avoid overestimating the frequency of autoimmune encephalitis. “We used diagnostic criteria from a 2016 position paper that are quite strict, and we included in the study only patients with definite or probable autoimmune encephalitis. To be extra cautious, we excluded cases of possible autoimmune encephalitis,” says Divyanshu Dubey, M.B.B.S., an autoimmune neurologist at Mayo Clinic’s campus in Minnesota who also participated in the study.

In addition, only antibodies highly specific for autoimmune encephalitis were included. “Other antibodies can be seen in small numbers of healthy individuals,” Dr. Flanagan says. “We excluded those antibodies because we didn’t want to over-diagnose.

“The prevalence that we report may actually be an underestimate,” he adds.

“We are discovering new antibodies all the time. Over the last 15 years, we have probably gone from one or two neural antibodies to 20 to 30 neural antibodies now available for testing. This allows us to diagnose autoimmune encephalitis more easily. Our ability to diagnose is likely to increase over time, so the prevalence of autoimmune encephalitis will also increase.”

The study also found that autoimmune encephalitis has a higher risk of relapse or recurrent hospitalization than infectious encephalitis. The risk varies according to the antibody involved but can be as high as 30%.

Pioneers in Autoimmune Neurology

Clinical Laboratory Technologist Nimo Mohamed performs a quality check on an active flow cytometry run.

Mayo Clinic has a distinguished history of translating discoveries about neural antibodies into advances in patient diagnosis and care. Much of the antibody testing in the encephalitis epidemiology study was conducted at Mayo’s Autoimmune Neurology Laboratory.

The most common antibody found in the study was myelin oligodendrocyte glycoprotein auto-antibody, also known as MOG IgG. That antibody is associated with acute disseminated encephalomyelitis, a disorder that often affects children. Other antibodies that were found include GAD-65, LGI-1, CRMP-5, NMDA-receptor, ANNA-2, and GFAP.

Clues to a possible autoimmune encephalitis diagnosis include:

  • New onset of epilepsy without an apparent underlying cause.
  • Autonomic dysfunction.
  • MRI findings of mesial-temporal-lobe involvement or inflammation in the white matter.
  • Recent diagnosis of cancer, which can trigger an immune response.
  • Faciobrachial dystonic seizures, which are associated with LGI1 antibodies.

“Knowing the antibody that’s involved in autoimmune encephalitis can give you a sense of the patient’s prognosis,” Dr. Flanagan says. “Some patients respond very rapidly to immunotherapy. They can go from being very confused to back to normal in a week. Antibody testing can help these patients to get their lives back.”

*Vora NM, Holman RC, Mehal, JM, et al. Burden of encephalitis-associated hospitalizations in the United States, 1998-2010. Neurology. 2014;82(5):443-451. DOI:


Barbara J. Toman

Barbara J. Toman is a Senior Communications Specialist at Mayo Clinic Laboratories. She is also the science writer for Mayo’s Neurosciences Update, Orthopedic Surgery Update and Pediatrics Update newsletters, which help referring physicians to stay informed about Mayo’s treatment and research. Barbara has worked at Mayo Clinic since 2007. She enjoys international travel and cooking.


A good step in assisting the physicians for a better management of their patients. Kudos to Mayo Lab for being a pioneer

Thanks for sharing this information. One subgroup of patients with autoimmune encephalitis you did not mention was the sero-negative group. Patients with sero-negative encephalitis can be very difficult to diagnose and this can delay their treatment or truncate it prematurely. I am speaking from experience, my then 13 y.o. son developed a non infectious encephalitis in 2013 and was partially treated during a 6.5 week drug induced coma to control his intractable seizures. He partially recovered after a 100 day PICU stay and 3 months of rehab at Spaulding Rehab Hospital. All anti-bodies panels have been negative to date. He suffered a relapse in June of 2014 and was treated with high dose Solumedrol and IVIG, with a remarkable response. What is your estimate of the incidence of sero-negative autoimmune encephalitis in the general population?

On behalf of encephalitis survivors and their loved ones around the world, we salute you… and, we thank you.

One evening in June 2017, my wife suddenly began showing the signs mentioned in your article : disorientation, confusion, forgetting names of familiar people and objects, etc. Suspecting a stroke, we took her to Mayo’s ER on the Phoenix campus. Pain in her head was so intense that she couldn’t speak, so it was futile to ask her to describe what she was feeling. The ER staff did the best they could, although one fellow told us that he’d often seen these same symptoms in OTHER people who were going through drug withdrawal. THAT was not appropriate and definitely did not describe my wife. Things were getting worse, not better, and then Dr. Cumara O’Carroll stepped into the room. By now it was about midnight. She was not on duty but had been called to the ER to see another patient. She’d finished with that consultation and was on her way home, but she had an impression to look into our room to see what the confusion was all about. After assessing my wife’s condition, Dr. O’Carroll instructed the ER folks to administer an anti-viral drip. My wife was admitted to the hospital, and, shortly thereafter, Dr. O’Carroll left.

Long story short: Lab analysis of my wife’s spinal fluid revealed the presence of the shingles virus, and this had caused encephalitis. The early administration of the anti-viral drip, even though the encephalitis had not yet been confirmed, was the key to my wife’s quick recovery — she was discharged three days later and has made a total recovery. It’s hard to describe the gratitude we feel for Dr. O’Carroll’s insight, treatment, and counsel.

Six months before this event, I had retired from the working world but soon found myself with too much time on my hands. Last December I found my dream job: I now work at Mayo in General Services as a courier. What a privilege it is to work in this terrific environment–to be surrounded by people who, like Dr. O’Carroll, are living examples of the Mayo’s mission: putting the needs of the patient before all else.

My 20 yrs old just experienced anti-nmda receptor encephalitis a few months ago. She was a very bright, healthy young lady in her 3rd year premed at the university. She came home for a visit just the weekend before Thanksgiving, and started complaining about headache on the left side of her head. We rushed her to the ER, at Halifax Hospital in Daytona Beach, Fl, and after doing a few tests, we were told that she was fine and just needed some rest. After 2 days, the headache became unbearable and we took her back to the ER. But by then, she had started to blink her eyes and the ER doctor told us that she was having seizures, which she never had before, and kept her overnight for observation. The next day, the neurologist came in and told us that he was moving her to the ICU so that she can be monitored with an EEG machine for the seizures. My daughter was almost her normal self before she was admitted to the ICU, except that she was blinking her eyes more often and hallucinating every now and then. The day after being in the ICU, on Thansgiving day this past yeat, the neurologist claimed that she was having seizure activity in her brain and decided to induce her in a coma and out her on a ventilator, so that he could put her on heavy doses of anti seizure medications and antibiotics. In the meantime, all her tests were coming out negative for bacterial infections for almost 2 weeks. She was finally taken off the ventilator after 10 dys but by then she was worse than when she went to the hospital. She wasn’t responding to us, not talking, not swallowing and just confused and agitated. She wax tied to the bed and the doctors kept giving her ativan and precedex to keep her comfortable and didnt have answers for me. That’s when I realized that I was going to lose my daughter if she stayed in that hospital. She had developed pneunomia and her health was detoriating and the neurologist, ICU doctors and the infectionist doctor had no idea what diseade she had, but were just pumping her with medications that were making her health worse They never even tried to give her any type of anti-vral medicines even though they knew that it wasn’t bacterial. With the help of one of the ICU doctor, who saw my daughter for just 2 days, she was finally transferred to the Neuroscience Institute at the Orlando Florida hospital. The neurologists at Halifax were very clueless while my daughter was lying there, on a hospital bed, and fighting for her life.
At the Orlando Florida hospital, Dr. Hyeong Lee and his team took over her case and saved her life. We found out that my daughter should have been started on steroidsat Halifax hospital once the doctors knew that she didn’t have any type of bacterial infection, but they had instead compromised her health more and which I believe almost killed her. Dr.Lee started my daughter on immuno-suppressants as soon as he saw her and told us he suspected that she may have an autoimmune disease on the very first day. Within a week, he confirmed to us that she had anti-nmdar encephalitis, even though she didnt have any ovarian cyst, teretoma, or any psychiatric symptoms. Dr.Lee worked with his team, along with a team of neuro-oncologists, and they used all their medical skills, their knowledge, and did their best to save my daughter’s life. They were the most caring and compassionate doctors and we feel so blessed to have met them.
After spending about 6 weeks bedridden at the Neuroscience Institute, my daughter had started to recover from the trestments dhe was getting and was able to recognize us on Jan 3rd. She was then discharged on Jan 19th, 2018. She’s still recovering and has regained back about 75% of her memories so far. She couldn’t remember much after she started getting better. I remember vividly how heartbroken I felt when she started crying because she couldn’t remember how to tell time on Jan 15th or even do simple maths problems.
My point in sharing part of my daughter’s ordeal with anti-mda receptor encephalitis is to bring more public awareness about this disease, so that more lives can be saved with the right diagnosis. The lack of knowledge about Anti-NMDA Receptor encephalitis among people in the medical field, and mostly among doctors, can be very scary. People affected by this disease can lose their lives unnessarily if the doctors don’t diagnose and treat them accordingly on time. I hope that more and more people educate themselves and learn about this disease by reading about it, and not by the way I learned about anti nmda receptor encephalitis. The more we share about our ordeals, the more we can help others avoid the pain and suffering that we went through. I honestly and sincerely hope that no other persons and parents have to ever go through the painful and scary journey my daughter and my family went through.

My 26 yr. Old daughter was diagnosed by the CDC in Amarillo Rd. June of 2017. He said it was highly probable she got it at Smithfield Genetics i n Pampa Tx. at her job inoculating the swine there. They terminated her and cut off all medical. She has tremors muscle weakness, slurred speech, displaying pupils, tires very easily, memory loss, slow comprehension and thought process. Her primary care physician in Pampa would no longer see her due to no insurance. I have spent my savings although as s my alot to try to get her seen. No benefits as of yet. Filed for ssi and sad in Jan. waiting for decision. She can’t hold a job because of her illness. So no unemployment. No indigent care as of yet she’s applied now 3 times. Ruth’s place said she’s too severe. Workmans comp said they won’t cover because its viral. Frustrated. Feeling no one cares and not willing to help. You never thought you would have to hand feed your once healthy daughter at 26. Just in tears. No where to turn. Overwhelmed.

Thank you for your comment, David. According to Dr. Flanagan, “In our study about half of those with autoimmune encephalitis did not have a neural antibody found. The incidence of seronegative autoimmune encephalitis was 0.4/100,000 person-years. We suspect that over time with medical advances and the discovery of new antibodies associated with encephalitis, some of these patients who were seronegative in our study may have antibodies that were not detectable previously. Retesting for antibodies can be considered in patients diagnosed many years ago with seronegative autoimmune encephalitis, as the rate of new neural antibody discovery is currently 1-2 per year.”

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