Diseases: This is an attempt at a comprohensive list for those diseases that inflict rats and the main organism that is responsible.
Bacterial...
Hemobartonellosis (Hemobartonella muris)
Mycoplasmal Arthritis (Mycoplasma arthriditis)
Mycoplasmosis (Mycoplasma pulmonis)
Pasteurellosis (Pasteurella pneumotropica)
Pseudomoniasis (Pseudomonas aeruginosa)
Pseudotuberculosis (Corynebacterium kutscheri)
Salmonellosis (Salmonella enteritidis)
Streptobacillosis (Streptobacillus moniliformis)
Streptococcocosis (Streptococcus pneumoniae)
Tyzzer's Disease (Bacillus piliformis)
Viral...
Kilham Rat Virus or KRV
Sendai
Sialodacryoadenitis or SDA
Parasitic...
Giardia (Giardia muris)
Hepatozoonosis (Hepatozoon muris)
Lice (Polyplax spinulosa)
Mites (Laelaps echidninus, Notoedres muris, Radfordia ensifera)
Pinworm (Aspiculuris tetraptera, Syphacia muris)
Sarcocystosis (Sarcocystis muris)
Spironucleus (Spironucleus muris)
Tapeworm (Hymenolepis diminuta, Hymenolepis nana, Taenia taeniaeformis)
Fungus...
Trichophyton mentagrophytes
Noninfectious...
Chromodacryorrhea
Mammary neoplasm
Ringtail

References...
www.lvma.org/rat.html
www.doctorfungus.org
www.radil.missouri.edu
www.allivet.com
www.ratguide.com
www.medilexicon.com
www.exoticpetvet.net