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Aside from the heavy smell left over from a bat colony guano itself can be harmful to humans and animals if left in a structure. Bats can carry histoplasmosis and it is transmitted in the lungs via spores after the guano is disturbed in some manner, typically through clean-up or even walking through it in an attic. Histoplasmosis is a fungal infection affecting the respiratory system and can be fatal. If the guano can be accessed or removed through a demolition process, it is recommended that it is removed or at least chemically treated.

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