The Collaborative International Dictionary of English v.0.48:

Pathogen \Path"o*gen\, Pathogene \Path"o*gene\, n. [See
   Pathogenic.] (Biol.)
   Any microorganism which causes disease; a pathogenic
   organism; an infectious microorganism; a bacterium, virus, or
   other agent which can cause disease by infection; -- opposed
   to zymogene. The spelling pathogene is now archaic.
   [1913 Webster + PJC]

Moby Thesaurus II by Grady Ward, 1.0:

37 Moby Thesaurus words for "pathogen":
   adenovirus, aerobe, aerobic bacteria, amoeba, anaerobe,
   anaerobic bacteria, bacillus, bacteria, bacterium, bug, coccus,
   disease-producing microorganism, echovirus, enterovirus,
   filterable virus, fungus, germ, gram-negative bacteria,
   gram-positive bacteria, microbe, microorganism, mold,
   nonfilterable virus, picornavirus, protozoa, protozoon, reovirus,
   rhinovirus, rickettsia, spirillum, spirochete, spore,
   staphylococcus, streptococcus, trypanosome, vibrio, virus