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I have a sentence where I need to add the preposition to occur, and I also need to know why it is so.

Ragpicker's disease occurred (preposition) individuals who handled rags that were woven with contaminated animal fibers.

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occur in is the correct way of expressing this meaning.

occur with and occur at are both grammatically correct, and this NGram indicates that they do occur in sentences.

If you look at actual instances, you will see that occur with is usually used when two things occur at the same time, for example:

Do any other symptoms occur with the cough?

Likewise, occur at is usually used when something occurs at a particular time or place, for example:

Figure 18.3 shows the respiratory and cardiovascular changes that occur at birth, beginning with the first breath.

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