By, through, with are comparable as prepositions followed by a word or phrase naming the agent, means, or instrument.
By is followed commonly by the agent or causative agency.
Through implies intermediacy; it is followed by the name of the person or thing that serves as the medium or the means by which an end is gained or an effect produced.
With, on the other hand, is often followed by the name of the instrument which accompanies the action.
It may, however, take for its object something not consciously used as an instrument but serving as the instrumentality by which an effect is produced.