I don't think that there is an etymological or technical difference
between those two words. By common custom, infestation has been used
when referring to the condition of an inanimate object (for instance,
"my house is infested with roaches"), whereas the latter term (infected)
is used with reference to a biological entity (for instance, "my patient
was infected with typhoid bacilli"). However, this distinction is not
based on any reason that stands up to scrutiny.