yes i have heard viruses and bacteria causing autoimmune. Such campylobactor can cause guillan barre,(pn and weakness, parylsis), pandas syndrome(strep throat), but these are rare though.Since your body is fighting an infection, the immune system requires alot of energy to fight it, and it uses up your fat, glucose protein. so your immune system basically exhaust itself. Parasitic infections are a different matter, parasites have to deal with your immune system when they infest you, smaller ones (microscopic) are treating like a regular infeciton. larger parasite like worms, and such have to suppress your immune system, so they can live inside you, so your autoimmune and allergies may go away. Though there are contrary to this, some worms can make your allergies, worst, i think this works with only specific parasites though.
Have you heard of the hygeine hypothesis, being in constant contact with microbes(bacteria,fungi,virus) at a young age protects you from autoimmune disease,cancer later in life. The western world suffers far more of these diseases than countries with poor sanitation,why? at a young age when your body is still developing immune system, it needs to be in contact in with certain microbes that are harmful and not harmful, so it can distinguish between them later in life. in a western world, young children are indoctrinated to believe a sterile environment is a clean and healthy environment, as a result more people get eczema, psoriasis, or immune related disorders.
an episode of monster inside me, showed where these people suffering from severe allergies, or autoimmune was completely relieved when they infested themselves with parasites. doctors do not approve of this, because theres no telling what parasites my do in the long run.