Normally its not actually mutation that can occur with using antibiotics or antimicrobialds. More likely you can have natural selection, in which those more resistant to those treatments are left to live an multiply. This is how things like MRSA or antiseptic resistant bacteria become rampant.
However it also happens that just like the finches of Galapagos the environment eventually causes mutations so to help organisms adapt to the environment which is how the strains of Antimicrobial resistant bacteria begin.