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Pathogenesis is disease. Normal flora are part of host's normal microbial community.

Primary pathogens infect healthy hosts. Opportunistic pathogens infect compromised hosts. Virulence is a quantifiable measure of pathogenicity. Parasites do not kill the host. Parasite: consume host resources at host expense. A parasite is an organism that lives in or on the living tissue of a host organism at the expense of that host, but without immediately killing the host. The biological interaction between the host and the parasite is called parasitism.

Parasitism is a type of symbiosis, by one definition, although another definition of symbiosis excludes parasitism, since certain types of DNA, such as transposable elements and B chromosomes, may also be considered as parasites of the host genome. Some organisms are parasitic only during a part of their lifecycle. Many cuckoos, for example, are brood parasites: their young are parasitic on the host species, but adult cuckoos fend for themselves.

AnthroponosisDisease with humans as only vertebrate hosts.
ZoonosisDisease transmitted among wild animals (reservoir hosts) and humans.
Reservoir HostWild animal that maintains infection in nature.
ProcyclicRelated to the beginning of the parasite's life cycle.
MetacyclicRelated to the infective stage of the parasite's life cycle.
VSGVariable surface glycoprotein
ESAGExpression site associated glyocoprotein
COGA bluster of orthologous genes (COG).
3-Way COGA 3-Way COG is orthologous between three species.
2-Way COGA 2-way COG is orthologous between two species. .
SyntenyA phenomenon where a COG consists of five or more genes.