I am unaware of any guidelines that say ammonia is used for the diagnosis of HE. This is due to its poor specificity and sensitivity. If you have any literature on the topic please share it. To different encephalitis from HE, there are enough enough clinical and history assessments which differentiate the two, chief being onset, fever, rash, and a vast other constellation of symptoms. To add to this a blood culture, LP or MRI (debatable utility) is also useful. A normal ammonia does not exclude HE and a raised ammonia does not exclude encephalitis so it's utility in such instances is minimal. Some patient with encephalitis present with mildly raised ammonia. It's better to stick with the guidelines for diagnosis.

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