Infest, overrun, beset are comparable when they refer to disagreeable or noxious things and mean to make trouble because of their presence in swarms.
Although infest carries only by suggestion the idea of annoyance or repugnance, since idiom does not require reference to the person so affected, the term is always derogatory.
Overrun is often interchangeable with infest, especially in the passive, but because it usually retains the implications of its basic sense it is the precise word when the idea of running or spreading is to be conveyed.
Beset has usually the meaning to trouble through frequency and persistence, and often connotes assailing or attacking.