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Instructions for users. This slide presentation provides an overview of the clinical manifestations and diagnosis of encephalitis. Below many of the slides, there are notes to explain the information in the slide. You should adapt the presentation for your own use.

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Instructions for users

  • This slide presentation provides an overview of the clinical manifestations and diagnosis of encephalitis.

  • Below many of the slides, there are notes to explain the information in the slide.

  • You should adapt the presentation for your own use.

  • If you want to present this topic in a more in-depth way, useful resources are listed at the end of the presentation.

Recognizing Encephalitis:Clinical Manifestations and Diagnosis

Learning objectives

Participants will:

  • Identify common causes of encephalitis.

  • Take a complete history from a patient with encephalitis.

  • Conduct a thorough physical examination for a patient with encephalitis.

  • Know the steps to conduct a successful lumbar puncture.

  • Identify the appropriate laboratory investigations for a patient presenting with encephalitis.

Clinical Case

Raj is a 5-year-old previously healthy boy who is brought in to his local health clinic by his mother with complaints of fever, poor appetite, and drowsiness.

  • What questions do you want to ask?

Photo credit: Dr. JulieJacobson

Clinical case- history

  • The patient’s mother reports a 3 day history of not eating and high fevers at night. He started vomiting this morning and complained that his “tummy” and head hurt.

  • Patient is not taking any medications. No one else is sick at home. Patient has received his routine immunizations.

    • What are important parts of your physical examination?

Clinical case- physical exam

  • Vital Signs

    • Temperature: 39.0, Respiratory rate: 42, Heart rate: 150

  • General: patient looks pale, clammy, and is lying motionless in his mother’s lap

  • Eyes, Ears, Throat: Left pupil slightly dilated, dry lips

  • Chest: tachypneic, clear

  • Cardiac: capillary refill > 3 seconds, no Murmur

  • Neurological: responsive only to painful stimuli, decreased tone throughout, symmetric hyperreflexia

    • What investigations would you do for this patient?

Clinical case- laboratory testing

  • Lumbar puncture

    • Cerebrospinal fluid (CSF): 850 WBC’s (80% Lymphocytes), glucose 80, protein 110

    • Anti-JEV IgM- pending

  • Patient’s clinical presentation and findings on CSF are more consistent with encephalitis than meningitis. An IV is placed and Raj is started on antibiotics and IV hydration. He becomes more alert and responsive. His CSF is sent to the state lab and comes back later positive for Japanese encephalitis.

What is encephalitis?

  • Encephalitis is an inflammation of the brain tissue due to infection.

  • Most often caused by viruses that pass into blood stream and then into cerebral spinal fluid, leading to destruction of neural cells and inflammation of brain parenchyma.

    • Primary or acute encephalitis

  • May also result from a viral-mediated inflammatory response in the brain following an acute, systemic infection.

    • Secondary or post-infectious encephalitis

Viral infections of the Central Nervous System (CNS) result in the following clinical syndromes:

Note: A single infection can affect multiple locations of the CNS, making clinical diagnosis difficult (i.e., meningomyeloencephalitis)

How to distinguish encephalitis from viral meningitis

  • Unfortunately, the clinical syndromes and results of routine laboratory tests are typically nonspecific and often do not help distinguish encephalitis and viral meningitis.

  • Patients may have symptoms of both parenchymal and meningeal processes.

    • i.e., A patient with stiff neck and photophobia, though classic signs of meningitis, could in fact also have encephalitis! (called meningoencephalitis)

  • It is important to recognize other infectious and noninfectious causes, particularly those which are treatable

Encephalitis vs. meningitis


Inflammation of brain parenchyma secondary to infection is known as?

  • Meningitis

  • Encephalitis

  • Neuritis

  • Epilepsy

What causes encephalitis?

  • Viruses (most common)

    • More than 100 different viruses can cause acute encephalitis

    • Seasonal and geographic distribution can help narrow differential diagnosis

    • Examples of common viruses:

      • Arboviruses

      • Enteroviruses

      • Mumps, Varicella

      • Herpes simplex virus

      • Influenza

      • Rabies

*Note: A large number of reported cases of encephalitis are due to an unspecified cause


  • Arboviruses or “arthropod-borne viruses” are the primary cause of encephalitis in many countries.

  • Arthropods that transmit the viruses include mosquitoes and ticks.

  • Common arboviruses include Japanese encephalitis, West Nile, and Dengue viruses.

  • Note: Unclear whether Dengue virus causes true encephalitis syndrome

Photo credit: Richard G. Weber

Japanese Encephalitis (JE)

  • Most important global cause of arboviral encephalitis with > 50,000 cases and 15,000 deaths reported each year.

  • Only about 1 in 250 JE infections result in symptomatic illness.

  • Primarily affects children 1 to 15 years of age.

  • Incubation period is 5 to 14 days.

  • If unrecognized, mortality is up to 30% with half of survivors sustain severe neurological sequelae.

Clinical approach to JE

  • JE classically presents as an acute encephalitis syndrome.

    • Fever, impaired mental status, seizures, flaccid paralysis

  • From a clinical perspective, encephalitis due to JE is indistinguishable from encephalitis caused by other agents.

  • Therefore, this presentation will focus on recognizing acute encephalitis in general.

Non-viral causes of encephalitis

  • Bacteria

    • Tuberculosis, cat-scratch disease, Brucellosis, typhoid fever

  • Spirochetes

    • Leptospirosis, Syphilis, Lyme disease

  • Fungi

    • Cryptococcosis, Histoplasmosis

  • Other infections

    • Cerebral malaria, Toxoplasmosis, amoebiasis


Which of the following is NOT a common cause of encephalitis?

  • Arbovirus infection

  • Herpes virus infection

  • Tuberculosis infection

  • Vitamin A deficiency

Who is at risk for encephalitis?

Anyone can get encephalitis. However, the following groups are at higher risk:

  • Young children or the elderly.

  • Persons with HIV.

  • Persons taking immunosuppressive drugs.

  • Persons living in encephalitis endemic areas.

Clinical approach to encephalitis

  • Understanding clinical manifestations.

  • Considering differential diagnosis.

  • Taking a good history.

  • Performing a physical exam.

  • Identifying treatable vs. untreatable causes.

  • Reporting suspected cases for disease surveillance.

Clinical manifestations of encephalitis

  • The clinical presentation of encephalitis is generally nonspecific:

    • Fever, headache, vomiting, occasionally accompanied by seizures, mental status changes, and/or focal neurologic deficits

  • Any patient presenting with fever and an abnormal neurologic exam should be evaluated closely for encephalitis!

Important signs of encephalitis to watch for in children

  • Vomiting

  • Body stiffness

  • Constant crying that may become worse when the child is picked up

  • Full or bulging fontanel (the soft spot on the top of the head)


Sudden fever


Change in consciousness

Irritability orrestlessness

Vomiting and diarrhea

Tremors or convulsions

Common symptoms of encephalitis

Differential diagnosis of encephalitis

  • Bacterial infection

  • Other infections

    • Meningitis, tuberculosis, brain abscess

    • Cerebral malaria, Rickettsial, spirochetal, toxoplasmosis

  • Intracranial hemorrhage or tumor

  • Trauma

  • Toxic ingestion

  • Hypoglycemia

  • Guillain-Barre syndrome


The following are common symptoms of encephalitis in children, EXCEPT

  • Seizures

  • Poor appetite

  • Bloody diarrhea

  • Fever

  • Lethargy

General principles of history taking

When taking a history, it is important to remember the principles of good communication:

  • Be respectful.

  • Use familiar words and phrases and avoid technical language.

  • Be patient - parents under stress may not remember well.

  • Find a translator if language is a barrier.

Steps in Conducting Patient history

  • Chief complaint (CC)

  • History of present illness (HPI)

  • Review of systems (ROS)

  • Past medical history (PMH), family history (FH), social history (SH)

Important questions to ask a patient presenting with symptoms of encephalitis

  • Any symptoms of a viral prodrome?

    • Upper respiratory infection symptoms, cough, malaise, decreased oral intake, diarrhea, nausea, vomiting?

  • Any recent exposures?

    • Ill contacts, travel history, occupation, pets, tick or mosquito bites?

  • Perform a thorough neurological review of systems (ROS)

    • Headache, photophobia, stiff neck, poor sleep, change in mental status, irritability, convulsions?

Example of History

  • CC:

    • What brings you to medical attention?

  • HPI:

    • When did you become sick?

    • What were the first symptoms and how have they evolved?

Example of History (2)

Example of History (3)

  • PMH:

    • Preexisting health problems?

    • History of abnormal chest X-ray?

    • Current medications?

    • Allergies?

    • Immunization status?

      • In particular JE, measles, mumps, Hib

  • FH/SH:

    • Any household members recently ill?

    • Any recent animal bites, exposure to toxins?

    • Any travel within the previous 2 weeks?


True or False. It is okay to skip the history if a family comes in and does not speak your native language.

  • True

  • False

Physical examination of a patient with suspected encephalitis

  • Assess ABC’s (airway, breathing, and circulation).

  • Rule out Cushings triad:

    • Hypertension + bradycardia + irregular respirations

    • This is a medical emergency! (indicates increased intracranial pressure and impending cerebral herniation)

  • Perform thorough neurological exam.

Emergency signs/Reasons for referral

  • Respiratory distress

    • Obstructed breathing OR central cyanosis OR severe respiratory distress

  • Shock

    • Cold hands with capillary refill > 3 seconds; weak, rapid pulse

  • Severe dehydration

    • Diarrhea plus two of these:

      • Lethargy

      • Sunken eyes

      • Very slow skin pinch

  • Coma or convulsions

Child with convulsions

Overview of physical exam (1)

  • Vital signs:

    • Temperature, heart rate, respiratory rate, blood pressure, weight

  • General appearance:

    • Drowsy, severe wasting, edema?

  • Skin:

    • Turgor, capillary refill, palmar pallor

    • Rash: petechiae, vesicles, bruising?

    • Diffuse adenopathy?

Overview of physical exam (2)

  • Head, eyes, ears, nose and throat:

    • pupils equal and reactive, corneal clouding, neck stiffness?

  • Heart:

    • gallop rhythm, slow heart rate?

  • Chest:

    • rales, crackles, signs of pneumonia, respiratory distress?

  • Abdomen:

    • enlargement of liver or spleen?

The neurological exam


The neurological exam in an encephalitis patient is part of the general physical examination. Thus, the neurologic exam should always be preceded by and interpreted in the context of a more general examination.

The neurologic exam

  • Mental status

    • Level of alertness:

      • AVPU scale for rapid assessment: Alert / Responds to voice / Reacts to pain / Unconscious

      • Glasgow Coma Scale or other coma scale

    • Orientation, memory, speech, etc.

    • Irritability, aphasia?

The neurologic exam (2)

  • Cranial nerves

    • Pupil reactivity, eye movements, fundoscopic exam for papilledema, facial muscles

  • Motor exam

    • Assess strength, tone of upper and lower extremities

      • Compare sides

    • Abnormal movements or posturing?

  • Sensory system

    • Assess pain, vibration, temperature sensation

      • Compare sides

Testing facial nerve (VII)

The neurologic exam (3)

  • Deep tendon reflexes

  • Coordination and Gait

    • Finger-to-nose test, Romberg test

    • Tandem (heel to toe) walking


Tandem walking

Romberg Test

Photo credit: Dr. Rao


At completion of physical examination

Based on symptoms and signs:

  • Provide an initial assessment.

  • Determine which laboratory tests are required.

  • Develop a care plan.

  • Communicate the information with the parents or caregiver.

  • Report suspected case of encephalitis to local health authorities!


Which of the following abnormalities in the neurological exam can be seen in a patient with encephalitis?

  • Decreased level of alertness

  • Abnormal movements of the lips

  • Paralysis of left arm

  • Abnormal finger-to-nose test

  • All of the above

Photo credit: Dr. JulieJacobson

Acute encephalitis syndrome (AES):

For surveillance purposes, WHO defines a case of acute encephalitis by:

  • An acute febrile illness, AND

  • A change in mental status (such as confusion, disorientation, inability to talk, coma) AND/OR

  • New onset seizures, excluding simple febrile seizures*

* Simple febrile seizure: a single seizure lasting < 15 minutes with recovery of consciousness within 60 minutes, in a child aged 6 months to 5 years.

Surveillance for cases of encephalitis

  • For surveillance purposes, JE is also commonly reported under the heading of “acute encephalitis”.

  • In WHO’s guidelines for JE surveillance, syndromic surveillance for JE is recommended. This means all cases of acute encephalitis syndrome (AES) should be reported.

  • Laboratory confirmation of suspected cases is done where feasible.


Which of the following is NOT part of the WHO case definition for acute encephalitis syndrome?

  • Fever

  • Change in mental status

  • Diffuse rash

  • New onset seizure

Laboratory studies of suspected encephalitis

  • Lumbar puncture

    • CSF analysis and culture

  • Blood, urine, secretion cultures

  • Serum and CSF antibody testing

  • Neurodiagnostic testing

    • Magnetic resonance imaging (MRI) or Computed Tomography (CT) scan

    • Electroencephalogram (EEG)

Importance of performing a Lumbar Puncture (LP) in a patient with suspected encephalitis

  • Collection and testing of spinal fluid are standard management for any patient with suspected CNS infection to direct treatment (e.g., if CSF profile suggests bacterial infection).

  • An LP should be performed by a skilled healthcare provider.

  • For detailed review of LP procedure and technique, see separate presentation.

Steps in performing a lumbar puncture

  • Obtain informed consent.

  • Gather materials.

  • Position patient.

  • Administer local anesthetic.

  • Insert needle with sterile technique.

  • Measure opening pressure.

  • Collect cerebrospinal fluid (CSF).

Relative contra-indications to lumbar puncture

  • Evidence of a space-occupying lesion such as a tumor or brain abscess.

  • Signs of increased intracranial pressure.

    • Unequal pupils, elevated blood pressure, slow heart rate, irregular breathing, posturing

  • Cardiopulmonary instability.

  • Soft tissue infection at puncture site.

  • Significant, uncontrolled bleeding disorder.

    *See note

Laboratory tests on CSF

  • Cell count, differential

  • Glucose

  • Protein

  • Gram stain

  • India ink preparation

  • Stain for acid-fast bacilli

  • Viral, bacterial, and fungal cultures

  • Anti-JEV IgM ELISA

  • JEV RT-PCR (if available)






0-5 WBC/mm3








+/- increased







40-80 mg/dl





< 40%


< 30%


5-40 mg/dl









Gram stain





Summary of typical CSF findings

CSF plasma : glucose ratio


Laboratory tests on blood:


  • Blood count, differential

  • Glucose

  • Electrolytes

  • Culture


  • Malaria smear

  • Serum anti-JEV IgM ELISA

  • Dengue serology

Additional laboratory tests to consider

  • Blood: liver enzymes, blood urea nitrogen, creatinine, ammonium, calcium, magnesium, blood gas

  • Urine: analysis, culture

  • Brain biopsy


Why is it important to perform a lumbar puncture on all suspected cases of encephalitis?

  • To get practice in the technique of performing a lumbar puncture

  • To inject life-saving medications into the spinal fluid

  • To identify treatable from non-treatable causes of encephalitis (i.e. bacterial infections)

  • A lumbar puncture should not be performed on patients with encephalitis


  • Depends on cause and severity of illness and patient’s age.

  • Mild cases recover in 2 to 4 weeks with supportive care.

  • Severe encephalitis can lead to numerous complications.

    • Hearing and/or speech loss, blindness, permanent brain and nerve damage, behavioral changes, cognitive disabilities, lack of muscle control, seizures, memory loss.


Which of the following are possible complications of encephalitis infection?

  • Paralysis

  • Hearing loss

  • Seizure disorder

  • Decreased intelligence

  • All of the above

Important points to remember

  • Acute encephalitis is a medical emergency.

  • Any patient presenting with fever and impaired mental status or neurological exam should be evaluated for encephalitis.

  • The diagnosis of encephalitis is clinical.

    • Don’t forget the value of a good history and physical exam.

  • All suspected cases of encephalitis should be reported to local authorities.


Gutierrez, KM, Prober, CG. Encephalitis: identifying the specific cause is key to effective management. Postgraduate Medicine. 1998;103(3):123-125, 129-130, 140-143.

Huang, C, Chatterjee, NK, Grady, LJ. Diagnosis of viral infections of the central nervous system. New England Journal of Medicine. 1999;340(6):483-484.

Kabilan L, Rajendran R, et al. Japanese encephalitis in India: An overview. Indian Journal of Pediatrics. 2004;71:609-615.

Mandell GL, Bennett JE, Dolin R, editors. Principles and practice of infectious diseases. Philadelphia: Churchill Livingstone; 2000.

National Institute of Neurological Disorders and Strokes (NINDS). Encephalitis and meningitis [fact sheet]. Bethesda: National Institute of Health; 2004. Available at:

Roos KL. Encephalitis. Neurologic Clinics. 1999;17(4):813-33.

Solomon, T, Dung, NM, Kneen, R, et al. Seizures and raised intracranial pressure in Vietnamese patients with Japanese encephalitis. Brain. 2002; 125:1084-1093.

U.S. Centers for Disease Control and Prevention (CDC). Japanese encephalitis [fact sheet]. Fort Collins: CDC; 2004. Available at:

Whitley, RJ. Viral encephalitis. New England Journal of Medicine. 1990;323(4):242-250.


Please include the following acknowledgement if you use this slide set:

This slide set was adapted from a slide set prepared by PATH’s Japanese Encephalitis Project.

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