Prions are protein complexes that can replicate and cause damage to tissues like nerves. Illnesses like bovine spongiform encephalopathy and Crutzfeld-Jacobs Disease are prion illnesses. There is evidence that other brain disorders like Alzheimer's and Parkinson's diseases are also prion induced. There is currently no cure for prion illnesses only treatments to slow the disease progression.
Viruses are pathogens that infect cells with their DNA and use the machinery of the host to make copies of themselves and build new viruses. Viral illnesses cannot be cured with antibiotics. They often elicit a strong non-specific immune response giving the infected individual a high fever and increased mucus production. The body's specific immune responses will learn to produce antibodies to fight viruses which is why you often can't get the same virus twice. This has led to the development of vaccines, which introduce a killed or similar virus to teach the immune system how to combat the virus before you actually get the disease. Chicken pox, small pox, colds, influenza, and Ebola are examples of viruses.
Bacterial illness is a pathogen where the bacteria disrupt cellular processes and attack healthy cells. This is often referred to as an infection. Antibiotics often are used to treat bacteria, but due to the process of natural selection, resistant strains can evolve. Gram negative bacteria which contain a double outer membrane and less peptidoglycan evolve resistance most rapidly. Untreated infections can lead to sepsis which is a potentially fatal condition. Strep Throat, MRSA, Anthrax and Staphylococcus infections are examples of bacterial diseases.
Fungus are eukaryotic pathogens related to yeast and molds. They often involve the skin, intestines or lungs where it easy for them to enter. The yeast or fungi begin to grow in tissue and cause inflammation and damage to the tissues. Examples of fungal diseases are athletes foot, jock itch, ring worm, thrush and fungal pneumonia.
Protista or Protozoans are single cell eukaryotes that invade the body and cause an inflammation response where they reside. Examples are giardia, amoebic dysentery and malaria.
Helminthes are flatworms that can invade and parasitize the body causing weakness and cramping. They usually reside in a place where there is ample oxygenated blood or digestive juices to feed on. Examples are Tapeworms and Liver flukes.