"... medical treatment would have involved vaccines and medicines that were developed after the microscope..."

Clearly I am not talking about vaccines, and am talking about medications otherwise under the unbrella term 'improved medical treatment'. And, amongst the primary mechanisms was indeed hygiene. Prior to the Civil War, doctors didn't wash their hands between patients much.

This is centuries after the invention of the microscope by Leeuwvanhoek in the 17th Century.