Two prominent literary devices that Daniel Defoe uses in A Journal of the Plague Year are symbolism and allegory.  Allegory is a rhetorical device that uses stories or pictures to convey hidden meanings.  Usually the meaning is a moral or political one.  Symbolism is more or less the same thing.  In A Journal of the Plague Year Defoe uses the rats as a symbolic stand-in for people.  The fate of the people is closely tied with the rats themselves.  When the rats are not doing well, dying all over the place and in general being miserable, it is safe to assume that the people will follow.  Later, when the rats begin to thrive, it can be interpreted as a positive sign that the people will follow. 

Another example from the story is Jacques's death.  There are a lot of religious parallels to Christ and Christianity associated with Jacques's death.  For example, the fever came onto him three times, which is significant in relation to the Bible and Christ's story.  Peter denied Christ three times before his death.  There were three people crucified that day.  Jesus prayed three times in the Garden of Gethsemane.