The best replacement for pathogen is antigen.

The best alternatives to pathogen are rated as following:
★★★★★  antigen
★★★★  parasite
★★  vundle
★★  disease
★  commensal
★  opportunistic pathogen
★  neobundle
★  opportunistic
★  toxin
★  microbe
  allergen

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Speaking about pathogen, one probably shouldn't forget about snipmate.

Other search terms related to pathogen and their ratings are:
★★★★★ snipmate
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pathogen
antigen
parasite