Infectious Disease Compendium



(IDSA Guidelines)

Altered mental status and a fever. Specific diagnosis depends on the organism.

Epidemiologic Risks

There are a host of reasons that people get encephalitis, depends of the cause.


Lots. The exposure history is everything in making the diagnosis.

Viral: Astrovirus (in the immunocompromised), Dengue, Eastern equine (mosquito vector), Enterovirus (5% in California, PubMed) Epstein–Barr virus, Herpes, Hepatitis E, Influenza (more in children than adults), Japanese Encephalitis Virus (mosquito vector), La Crosse, Lymphocytic choriomeningitis (Hamster vector), Measles, Mumps, Murray Valley, Nipah, Parvovirus, Powassan, Rift Valley, Rubella, St. Louis (mosquito vector), Toscana (PubMed),Vaccinia, Varicella–zoster, Venezuelan equine (mosquito vector), West Nile (mosquito vector), Western equine (mosquito vector). And more.  

Every part of the world has its odd virus that can melt the brain, like the Variegated Squirrel (A pet in Germany, the squirrel comes from South America) related Bornavirus (Really I can't make that kind of stuff up).

In the US NE there is deer tick virus encephalitis (PubMed).

Beware. As the world warms the range of vectors and their pathogens are a changing (Pubmed). So just because a pathogen wasn't in the area last year doesn't mean it hasn't arrived. Some things can't be stopped by a wall.

Non Viral: Some important causes but by no means inclusive: Acanthamoeba, Actinomycosis, Ballamuthia mandrillaris, Baylisascaris, Brucella, Cat–scratch disease, Chlamydia, Cryptococcus, Ehrlichia, Histoplasma, Legionella, Leptospirosis, Listeria, Lyme, Mycoplasma, Naegleria, Nocardia, Orientia tsutsugamushi (In India (PubMed), Plasmodium falciparum, Q fever, Relapsing fever, Rocky Mountain spotted fever, Syphilis (meningovascular), Toxoplasma, Trypanosomiasis, Tuberculosis, Typhus, Whipples disease. And more.

Transplanted organs have lead to West Nile virus, rabies virus, lymphocytic choriomeningitis virus, and Balamuthia mandrillaris amebae (PubMed).

In encephalitis with seizures, personality changes, autonomic dysfunction and speech problem, think of Anti-NMDAR, where antibodies directed against teratomas cross react with limbic brain. "Anti-NMDAR encephalitis was identified 4 times as frequently as HSV-1, WNV, or VZV and was the leading entity identified (PubMed). Besides serology (blood and CSF), you can use cryo-auscultation. Put the patient in a cold room and listen for teeth chattering in the teratoma. Old joke. The syndrome can be triggered by HSV encephalitis.

From a 2006 review in CID (PubMed) "A confirmed or probable etiologic agent was identified for 16% of cases of encephalitis: 69% of these agents were viral; 20%, bacterial; 7%, prion; 3%, parasitic; and 1%, fungal. An additional 13% of cases had a possible etiology identified. Many of the agents classified as possible causes are suspected but have not yet been definitively demonstrated to cause encephalitis; these agents include M. pneumoniae (n=96 ), influenza p 96 virus ( n=22), adenovirus ( n=14), Chlamydia species ( n=10), and human metapneumovirus ( n=4). A noninfectious etiology was identified for 8% of cases, and no etiology was found for 63% of cases."

As part of IRIS, HIV patient can get a CD8 encephalitis (PubMed) that is treated with steroids.

Empiric Therapy

You always treat Herpes if you think it is a viral encephalitis as it is the one you can treat. Otherwise its support and specific treatment depending on what you suspect from the history.


An important non-infectious disease cause, as if there is anything that is not infectious could possibly be important, is NMDA antibody disease, which causes maybe 1% of encephalitis in the young (PubMed)(Review).

Long term prognosis is poor, at least half have some kind permanent impairment (PubMed).

Curious Cases

Relevant links to my Medscape blog

Miss the diagnosis once, shame on me, miss it twice, Fool me — you can't get fooled again.

A Pres-ing diagnosis

Never Heard Of It

Summer time is encephalopathy time

Late Encephalopathy

Word Salad

Rich Little is Second


Last Update: 07/05/18.