A pathogen, germ, or bug was a disease-causing biological agent.
According to Doctor Phlox, germs were "among the most resilient organisms known to medical science." They could survive almost anywhere -- on kitchen counters, under fingernails, and in some cases the vacuum of space.
By 2151, over 200 million space-dwelling microbes had been cataloged. One such microbe called Polycocyx astris lived inside grains of interstellar dust and was one of the most virulent species, which could drift in a dormant state for millions of years and still cause a cold. (ENT: "Breaking the Ice")
This definition of germ also appears in the Star Trek Encyclopedia, 4th ed., vol. 1, p. 303. Added is, that a germ is "any of a wide range of unicellular microorganisms, including many disease pathogens. Also called microbes. Germs are microscopic in size."
Some germs spread with personal contact. In 2373, Elias Giger refused to shake hands with Jake Sisko, as it might spread germs. (DS9: "In the Cards")
Icheb was genetically altered by the Brunali to carry a pathogen that was lethal to the Borg. (VOY: "Child's Play")