Which preposition(by or with) will be used?

Solution 1:

You can say

• I was struck by [the] flu. (simple past tense—you might have recovered already)

But

• I am stricken with [the] flu. (past participle as predicate modifier—you currently have the flu, and are feeling horrible)

Of course, if you didn't want to sound so melodramatic, you could say:

• I am down with the flu (confined—mostly—to bed)

• I am fighting the flu (struggling, but probably not confined to bed—maybe even working, but suffering some symptoms)

• I have the flu (no indication of severity)

• I caught the flu (no indication of severity, nor of whether you have recovered)