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Decontaminator will burn out the spore clusters automatically so long as at least one is employed and there's Biogas.
Pest Control can harvest eggs from Sporemoths/Elefleas (and replant them if you want), and can be set to do that automatically. To remove a grown Sporemoth, Eleflea, or Plague Gnat you have to have Pest Control built and at least one worker assigned, plus Biogas for them to use, and then mark the actual bugs to be harvested (either individually or by using the Harvest selection tool. There's no automatic removal of the bugs though- you have to issue the harvest order.
Internal parasites like Sandworms, Tapeworms, or Rock Burrowers require either an Injector and one dose of Insecticide per parasite to remove, or you just have to wait for them to die off naturally while you deal with the side effects. Pest Control and the Decontaminator can't touch them.